Son silenced a sell-out crowd of more than 40,000 in Shenzhen with two goals in the first half, the first a penalty and the second a clever header from a corner just before half-time.
South Korea wrapped the game up in the dying minutes through a bullet header by Jung Seung-hyu - from a Son set-piece - and top Group C with a perfect six points.
Jurgen Klinsmann's side thumped Singapore 5-0 last week to begin their qualifying campaign in style and they were in much the same mood against an outclassed China.
With attacker Son looking in the groove, the Koreans dominated and were ahead after 11 minutes.
Wolverhampton Wanderers forward Hwang Hee-chan was brought down in the box and Tottenham Hotspur's Son duly stroked home the penalty.
It was all South Korea. Forward Cho Gue-sung headed just over the bar when unmarked from a corner and Son stung the palms of overworked goalkeeper Yan Junling.
Hwang In-beom's direct free-kick fizzed just past Yan's post midway through the half but China should have been level three minutes before the break with their first real chance.
South Korean full-back Lee Ki-je was dispossessed and Liu Binbin crossed for Tan Long, but the Chinese forward's first-time snap shot went narrowly wide.
They were to regret it on the stroke of half-time.
Son, who had been denied moments earlier by the legs of Yan, leapt unmarked from a corner to direct his deft header back across the China goal and into the far corner.
South Korea, who reached the last 16 of the 2022 World Cup, should have gone 3-0 ahead soon after the restart but China defender Zhu Chenjie cleared off the line, before Jung put the game to bed late on.
In other Asian World Cup qualifiers, North Korea thrashed Myanmar 6-1 away and Tajikistan won in Pakistan by the same scoreline.
Later Tuesday, Australia face Palestine in Kuwait, Japan play Syria in Jeddah and India host Qatar.
The top two from each of the nine groups in Asian qualifying for the World Cup in North America will progress through to the final qualifying stage.
