It is quite important for lake protection and treatment to find out if thermal stratification in summer has effect on the physical and chemical index of the water body. As for deep plateau lakes, water temperature differs greatly at different times during the day. To understand thermal stratification law and to know if the physical and chemical index such as total phosphorus (TP) and dissolved oxygen (DO) concentration, pH, etc. would vary with thermal stratification, we chose 6 sites of Lake Yangzonghai, a typical deep lake in Yunnan-Guizhou Plateau in summer, then measured water temperature, phycocyanin, DO, pH and chlorophyll-a every meter. At the same time, the layering water samples were also analyzed in the lab, and the concentration of TP was got. The result shows that (1) In the forenoon of summer clear days, the water body had no clear thermal stratification; When it was in the noon, the thermal stratification turned into 4 layers, and then 3 layers; At 14:00, the water body was stably stratified; When the thermal stratification is stable, the thermocline is between 9-13 m; the max temperature difference between epilimnion and hypolimnion is 7.8℃; (2) DO and pH has almost the same vertical stratification trend as the water temperature, and the stratification of DO and pH is synchronize with the water thermal stratification; (3) The algae and phytoplankton stratified with water thermal stratification, but it shows a time lag, the time lag is about 2 hours; (4) The TP is not sensitive to thermal stratification, the concentration of TP only sharply increase when it was very close to the bottom of lake. The concentration of TP is even above 9 m. And the disappearance of thermal stratification does not affect the concentration of TP. The average TP concentration of the whole lake is 0.033 ±0.03 mg/L.