Based on the expedition data obtained by the Pacific Oceanological Institute within the framework of the long-term collaborative Russian–Vietnamese investigations, analysis of the thermohaline structure of the South China Sea in different seasons was carried out. Three types of water structure were distinguished. These structures are formed as a result of water exchange through the straits and the following water transformation in the sea. A dependence of hydrographic conditions in the sea on the seasonal change of monsoon winds is demonstrated. Periods of monsoon wind changes correspond to a rearrangement of the currents. Water exchange through one or another strait is observed in the South China Sea depending on the seasonal circulation that corresponds to the intensity and direction of the monsoon. The seasonal variability water circulation defines the seasonal variability of water mass characteristics as well as the peculiarities of distribution of various types of water structure.