Radiolarians are planktonic protozoon that play an important role in marine ecosystem and paleoenvironmental construction. The South China Sea (SCS) and Malacca Strait (MLS), strongly influenced by the East Asian monsoon, are the key gateway between the Pacific and Indian Oceans. However, a few plankton studies of radiolarians are performed during winter and spring in the SCS and MLS due to the adverse sea conditions. In this study the use of a ship-board plankton net rendered it possible to obtain shallow water samples (~5 m depth) along transects from the northern SCS to MLS during the spring of 2017 and winter of 2017-2018. The results show that partitioning among Spumellaria, Nassellaria and Collodaria radiolarians differed spatially and seasonally. The high partition of Collodaria and low partition of Nassellaria are potential indicators of the strongly stratified waters with low nutrients for paleoceanographic studies in the slope and basin SCS. The radiolarian assemblages in the MLS are quite different from those in the SCS, that is, the two communities are largely independent, suggesting that advective transport between the MLS and SCS is rare. There are obvious seasonal variations in species diversity and abundance in both the MLS and SCS, generally with higher biodiversity and maximum abundances in winter. The results of Q-mode cluster analysis showed that radiolarian assemblages during winter were grouped together in the slope and basin SCS, and their distributions had moved to the southwest relative to those in spring. The results demonstrate the East Asian monsoon has a significant controlling effect on radiolarian diversity and geographic distribution in the studied areas. We also established five candidates for weakly stratified waters with high nutrients: Archiperidium hexacantha, Acanthodesmia vinculatus, Peromelissa phalacra, Dictyocoryne muelleri, and Tetrapyle octacantha. Thus, this study increases the knowledge of radiolarian geographic distribution in the tropics as a whole, as well as revealing the sensitive response of radiolarians to the regional environments, a fact which may prove useful for reconstructing the paleoceanographic changes.