The state of the natural environment of the marginal seas of the Northwest Pacific is largely controlled by the interaction of the atmospheric and hydrophysical processes. Tropical cyclones (typhoons), originating in the tropical zone of the Northwest Pacific and over the South China Sea basin, occupy a special place among atmospheric processes. The main destructive impact of typhoons falls on Southeast Asia. However, a significant number of are moving to the Russian Far East. The region of the South China Sea plays a significant role in the formation of tropical cyclones. This determines the importance of studying hydrometeorological processes not only in the Far East, but also in the South China Sea, and the need for cooperation between Vietnamese and Russian scientists. The main hydrodynamic structure of the western South China Sea is the Vietnamese Coastal Current (Western Boundary current), which depends not only on the seasonal monsoons but also on typhoons. The paper presents the results of joint Russian–Vietnamese studies of the dependence of the vertical structure of the Vietnamese Coastal Current on the Pacific tropical cyclones that form in the South China Sea. The study is done with numerical modeling. The period from April to June 1999 was used for modeling, provided with the necessary field data. The simulation results showed that, in general, the structure of water masses depends on the trajectories of tropical cyclones. In all cases considered, the Vietnamese Coastal Current is not a single flow, but represents a zone of eddy structures of different directions. An exception is the only situation in the condition of a tropical cyclone in the central region of the South China Sea when this current acquired the form of a single continuous flow directed from north to south only in the 200-m layer. The general patterns of changes in the dynamic structure of the Vietnamese Coastal Current for all the considered tropical cyclone trajectories include the following: areas with water transport in the northern direction prevail on the surface, while the rest of the water mass continues to flow generally in the southern direction. This transport of surface waters may be due to the influence of the emerging summer monsoon, and the rest of the water mass, which is less exposed to the still weak atmospheric processes of the monsoon type, continues to flow in the winter regime.