This paper reports the distribution of natural radionuclides of Ra-224,Ra- 223 in the surface water and stratified waters of the Luzon Strait and its adjacent waters during the cruises of September 2015 and May 2016. To understand the impact of the Fukushima nuclear accident, the artificial radionuclide Cs-137 in the waters was also analyzed. The results showed that the activities of Ra-224,Ra- 223 and Cs-137 were all within the natural radioactive background levels of the marine environment in the South China Sea. Ra-224 had a higher activity level in the water of the north South China Sea to the west of the Luzon Strait, and a lower activity level in the oceanic Philippine Sea to the east. The Cs-137 activity had no obvious spatial trends. Based on the vertical trends of Ra-224, Cs-137, and water temperature and salinity at three stations (LS3, LS5 and LS8), the distinct characteristics of the activity levels and gradients of Ra-224 and Cs-137 among the tropical surface water, subsurface water and mid-deep water were revealed. Typhoon Rainbow event reversed the overall circulation of the Luzon Strait and its adjacent area. A huge amount of western Pacific water characterized by low Ra-224 activities flooded into the South China Sea, reducing the activity level of Ra-224 in the waters. However, there were no significant differences of Cs-137 activity between the West Pacific and the north South China Sea, and ocean current changes had no effect on the Cs-137 activity levels of the water bodies.