Song touched the wall in 59.19 seconds, beating the previous record of 1:00.45 set by Australia's Peter Leek in 2010 on Friday,reports Xinhua news agency.
Fellow Chinese swimmer Xu Haijiao grabbed silver in one minute 0.08 seconds with Yang Guanglong, also of China, securing bronze in 1:01.18.
It was the 23-year-old's second Paralympic gold medal after his triumph in the 4x100m medley relay 34 points at the London Games in 2012.
Song's right arm was amputated when he was eight after he received an electric shock.
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