The statistical analysis results of CTD measured data of water mass in summer and autumn from the sea area of the Zhongsha Islands show that the sea surface temperature of seawater in the study area is between 30.0 and 31.2 °C, and the highest temperature distributed in the platform of the Zhongsha Islands. The sea surface salinity is from 33.6 to 34.1 PSU, and the highest salinity distributed near the Dong Island. The bottom temperature is from 1 to 25 °C, and salinity from 34.1 to 35.2 PSU, the highest salinity distributed in the southeast corner of the study area. In general, the temperature-salinity structure of the study area is characterized by high temperature, low salt in the surface layer and low temperature, high salt in the bottom layer, and the depth of mixed layer is between 20 and 90 m. The vertical velocity of surface, middle and bottom water in the study area is different, and the velocity is between 0.01 and 0.22 m/s. The seasonal variation characteristics of temperature and salinity in the study area were analyzed according to the FVCOM model. In winter, the sea surface temperature in the south of the study area was significantly higher than that in the north, and the temperature difference between the north and south was obvious. In summer, the distribution of sea surface temperature and salinity is obviously affected by typhoon, and the spatial distribution of sea surface temperature tends to be uniform. The numerical simulation results show that the intensity of flow field in the study area is strength in winter and summer, and weak in spring and autumn. The simulation results also show that extreme weather has a significant effect on the temperature and salinity structure in the study area in a short term, which is manifested as the decrease of sea surface temperature, the increase of mixed layer depth, and the enhancement of vertical mixing effect of water body.