A South Korean guardsman shot the man in the stomach with a handgun after he violently resisted inspections in the waters off South Korea's western coast, said coast guard official Kim Hye-gyeong.
The 45-year-old Chinese national was airlifted to a hospital and pronounced dead about 30 minutes later, according to officials at the Mokpo Hankook Hospital. The hospital did not immediately announce the exact cause of death.
The deadly fight occurred as a dozen South Korean coast guard officers boarded the Chinese ship for searches in South Korea's exclusive economic zone, which extends 200 nautical miles (370 km) from shore.
It wasn't immediately known whether there were other injuries.
Chinese fishing boats have been going farther afield to feed growing domestic demand for seafood as catches have decreased in waters close to China's shores. South Korea's coast seized about 220 Chinese ships last year for illegal fishing in the Yellow Sea.
In 2011, one South Korean coast guard officer was killed in a clash with Chinese fishermen in South Korean waters.