Abstract: The Zhongsha Islands mainly consist of the Zhongsha Atoll and Huangyan Island, particularly its adjacent sea water temperature and salinity, are of great significance for fisheries production, navigation security and underwater telecommunication. In the transitional period from spring to summer, significant seasonal variation in water temperature and salinity and corresponding thermocline structure can be observed in the region. Based on the CTD survey in the adjacent waters of the Zhongsha Atoll and Huangyan Island in May 2019 and June 2020, the water temperature and salinity distribution and difference are analyzed separately for the spring to summer monsoon transition in 2019 and post summer monsoon onset in 2020. Thermocline change is also analyzed with sea surface heat flux and satellite altimetry data. The results show that the water temperature in the Zhongsha Atoll rises rapidly after the onset of summer monsoon in 2020, and the temperature of each layer is higher than that during spring and summer monsoon transition period in 2019. The bottom temperature rises most significantly. The distribution of water temperature and salinity in the middle and upper layers near the Huangyan Island is similar to that near the Zhongsha Atoll in May 2019, but the those in bottom layer are different, and the depth of thermocline is also deeper. The bottom temperature rises most significantly in 2020 due to the onset of summer monsoon. The thermocline depth in 2020 is shallower than that in 2019. The horizontal temperature gradient near the Zhongsha Atoll is larger in 2019, which increases with water depth, but decreases gradually after the onset of summer monsoon in 2020. The horizontal distribution of salinity near the Zhongsha Islands in 2019 and 2020 is similar to that of temperature. The distribution of sea surface heat flux shows that the ocean heat absorption in the southwest of the atoll in May 2019 is higher than that in the northeast, thus the surface temperature is higher in the southwest and lower in the northeast. From June to July 2020, the ocean heat absorption in the southwest of the atoll is lower than that in the northeast, thus the surface temperature is lower in the southwest and higher in the northeast, consistent with the observations. In addition, the satellite altimetry data during the survey period shows that, due to the effect of mesoscale eddy, low temperature and high salinity or high temperature and low salinity waters are generated locally near the Zhongsha Atoll, resulting in the deepening of thermocline in most areas of near the Zhongsha Atoll in June 2020.