Headers from Koki Ogawa and Ko Itakura put runaway group leaders Japan two goals up at half time before Lin Liangming pulled one back for China early in the second half.
Ogawa snuffed out China's hopes of a comeback with his second of the game six minutes later to silence the crowd of 45,000 in Xiamen.
Loud booing greeted the Japanese national anthem before kick-off and the game was briefly stopped in the first half when a fan invaded the pitch.
"It was tough at times and we knew that the opening goal was going to be key," said Dutch-based striker Ogawa.
Japan were playing their first senior international in China in nine years and there is a long history of rivalry between the two countries.
There was a heavy police presence outside the Xiamen Egret Stadium, where about 750 Japan fans were expected to be in attendance.
"All the players got us this win today," said Japan coach Hajime Moriyasu.
"The players on the pitch, the players on the bench and those that weren't on the bench today -- it was down to their energy that we won."
The convincing victory gave Japan five wins and a draw in Asian qualifying Group C and took them to within touching distance of a place at the 2026 World Cup.
The top two teams in each of the three groups will reach the showpiece in the United States, Canada and Mexico.
Second place in Group C is wide open after Indonesia stunned Saudi Arabia 2-0 in Jakarta with Marselino Ferdinan scoring either side of half time.
It left Australia, Indonesia, Saudi Arabia and China all on six points ahead of the Socceroos' visit later Tuesday to Bahrain, who have five.
Short-lived joy
Japan made several changes to the team that beat Indonesia 4-0 on Friday with Brighton's Kaoru Mitoma and Crystal Palace's Daichi Kamada among those dropping to the bench.
Ogawa opened the scoring in the 39th minute, planting a firm header past goalkeeper Wang Dalei direct from a corner.
Japan doubled their lead just before the half-time whistle and again it came from a corner.
Koki Machida flicked on Junya Ito's delivery and Itakura was unmarked at the back post to nod the ball home.
Despite being behind China gave a much-improved performance after losing 7-0 to Japan in Saitama in their opening group game.
The hosts pulled a goal back three minutes after the break.
Xie Wenneng cleverly dummied Wei Shihao's pass and Lin slotted the ball past goalkeeper Zion Suzuki.
China's joy lasted just six minutes before Ogawa headed in another Ito cross to restore Japan's two-goal cushion.
Japan are home to Bahrain and Saudi Arabia in their next fixtures in March, with the World Cup within grasp.
"These last two games were difficult as we expected, but it was really positive to get two wins," said Itakura.
"There are lots of things we need to improve but it was positive and we'll get ready for the next games."
