The 17-year-old Kim clocked the winning time of 1:46.26 at Obihiro Forest Speed Skating Rink, some 200 kilometers east of the main host city, Sapporo.
Takuro Oda of Japan took the silver, half a second behind the South Korean.
Japanese Taro Kondo had the bronze in 1:47.88.
Kim earlier won the team pursuit gold with Lee Seung-hoon and Joo Hyong-jun on Wednesday.
Japanese skaters finished 1-2 in the women's mass start, as Miho Takagi timed 8:21.81, 0.07 seconds ahead of second-placed Ayano Sato.
South Korea's Kim Bo-Reum got the bronze in 8:47.46.
Chinese skaters Guo Dan and Han Mei finished fifth and seventh respectively.