The thermal stratification and its potential impacts on the phytoplankton biomass were studied through the four seasonal field investigations (October 2014-July 2016) in Lake Chenghai and Lake Yangzonghai, two mesotrophic deep lakes on the Yunnan Plateau, southwest China. The results revealed that these two lakes are both warm monomictic lakes, where the vertical stratification was occurred in spring, stabilized in summer and autumn, and disappeared in winter. The mean values of thermocline depth (the upper boundary), thickness and strength during the stratification periods (spring, summer and autumn) were 17.70±3.89 m, 5.54±4.44 m and 0.67±0.43℃/m in Lake Chenghai and were 12.53±3.35 m, 8.25±4.85 m and 0.53±0.43℃/m in Lake Yangzonghai, respectively. During the stabilized thermal stratification periods, the dissolved oxygen in the bottom of the water column reached less than 3 mg/L even 1 mg/L, and the specific conductance in the bottom was generally larger than that in the surface water column. In these two lakes, the maximum values of the seasonal-average algal biomass (represented by chlorophyll-a concentration) were both in winter, which was 19.22±11.08 μg/L in Lake Chenghai and 45.82±9.41 μg/L in Lake Yangzonghai. Moreover, the fading of thermal stratification may be an important factor that increases the inorganic nutrients in the surface of water column (from the bottom of water column). Thereafter, higher nutrients combined with suitable light conditions and water temperature could promote the occurrence of algal blooms in winter. Besides a certain similarity, the major influencing factors of seasonal phytoplankton biomass also had inter-lake and seasonal heterogeneity during the other periods of season changes.