The two-time Olympic champion was in fierce form, beating Uno Shoma by 35 points with Kagiyama Yuma third. Takahashi Daisuke and Muramoto Kana lie second in ice dance.
Hanyu Yuzuru is Japanese national champion once more.
The two-time Olympic champion won his first national title in five years and his fifth overall with two magnificent skates, the second set to a chilling "Heaven and Earth" as he scored a 319.36 to beat four-time defending champion Uno Shoma, who totalled 284.31.
Teenager Kagiyama Yuma, the Youth Olympic Games champ, was third, scoring 278.79.
It's a triumphant result for Hanyu in Nagano, who had come back to his home in Japan for much of the 2020 year during the COVID-19 pandemic, training away from his base in Toronto with his coach Brian Orser and team there.
"Thank you so much to my coaches and choreographers, I can feel you," he said to the TV cameras as he received his scores in the 'kiss and cry'.
This will ensure Hanyu a trip to March's World Championships in Stockholm, where he will bid for a third title after victories in 2014 and 2017.
He returned to Japan in the midst of the pandemic and had his programs choreographed over video with Jeffrey Buttle and Shae-Lynn Bourne.
Having been beaten by Uno at nationals a year ago and not skating since February - when he won his first Four Continents crown - it was unclear how he would perform on Japan's main stage.
But after an eye-popping rock genre skate in the short program to Robbie Williams' "Let Me Entertain You", he turned the entertaining to a more subtle, intricate and flowing page in the free skate, "Heaven and Earth" by a Japanese composer, which is full of nods to his culture, country and art that has made him so good.
Great not good was Hanyu's jumping on the day, too, hitting a quad loop, quad Salchow, triple Axel-double toe loop combination, quad toe-triple toe combo, quad toe-Euler-triple Salchow combo and triple Axel, all of which received positive grades of execution (GOEs) from the judges, adding up to his monstrous 215.83 free skate score.
He also outscored second-place finisher Uno in the program components (artistic marks) by some six points, registering nines and 10s across the board in what was a truly memorable skate, Hanyu bowing to each side of the arena in appreciation for his fans on site and around the world.
"I was happy I was able to perform this program well in these circumstances. Even though I have been training alone, there were a lot of people supporting me," he told reporters in Japanese.
"I have been training alone for a long time and still have some issues in my short program. But today I felt at ease. And I believe spectators also felt the same because I was able to perform as myself. So I felt confident about the way I have been training and that it wasn't wrong."
"Today I felt at ease." - Hanyu Yuzuru
Uno Shoma should walk away proud of his skating as well, the PyeongChang silver medallist having not competed since winning at this very event a year ago.
He has been training with Stephane Lambiel in Switzerland, and did not get to skate in the Grand Prix Series when the event in France was cancelled due to COVID precautions.
After a fall in the short program, Uno sat third and brought his best to the free skate, performing to a cover of Robyn's "Dancing on my Own".
He moved with grace and strength on the ice throughout, connecting to the music, and fought hard through a hand down on a quad toe midway through his program, landing four quads in total.
Uno also sported a broad smile during much of his routine, showing just how pleased he was to be back on the ice.
"Thank you," coach Lambiel told him in the 'kiss and cry'. "These are strange circumstances and you were peaceful, calm and happy. Your expressions were really good. It was a wonderful experience for everybody."
Uno said to reporters afterwards: "I didn't feel nervous and was totally calm," and added that he would like to take part in "as many competitions as possible" prior to Beijing 2022 and "grow as I compete".
He said of Hanyu: "By competing after a long time, it made me realise how great he is and gave me motivation to push myself further."
It was a strong showing for Kagiyama, as well, who has had a breakout last 12 months and will look to make his debut at Worlds in March.
With his father, Masakazu, a two-time Olympian, as his coach, Kagiyama has gone from junior national champion to now a two-time senior bronze medallist, winning at Lausanne 2020 in January, bronze at Four Continents and also his first senior Grand Prix gold at NHK Trophy last month.
Skating to an Avatar and The Lord of the Rings medley, Kagiyama shone during his free skate landing three quads and not letting a couple of shaky moments deter him. With maturing spins and step sequences, the experience of skating after Uno and before Hanyu will only help him moving forward.
Three-time national medallist Tanaka Keiji was fourth, some 40 points behind Kagiyama at 238.83, while reigning junior national champ Sato Shun placed fifth, scoring 236.51.
In the ice dance event, NHK Trophy winners Komatsubara Misato and Koleto Tim lead after the rhythm dance, skating to first place with a 71.74.
It was a strong showing for Vancouver 2010 bronze medallist in singles, Takahashi Daisuke, and his new partner Muramoto Kana. They overcame a mishap in practice to score a 67.83 and sit in second place.
Warming up in the morning, Takahashi fell on Muramoto's leg, an incident which put their participation in doubt.
"I didn't know what happened. But I felt the whole weight of his body and that was something I had never felt before," Muramoto told reporters. "So I thought to myself, 'This is bad.'"
"We had an accident this morning and we were not sure about competing. It was challenging mentally," Takahashi added. "So, I feel relieved that we could finish the program."
The duo said they worked on skating more freely versus how they did at NHK Trophy, where they were third out of three teams.
Komatsubara and Koleto made a strong start as they bid for a third consecutive national title with Fukase Rikako and Cho Eichu Oliver third, five points behind Muramoto/Takahashi.