Variation of water temperature is a critical physical property of a lake, which has great significance for other research, such as lake water quality, energy cycle, aquatic ecosystem. Illustrated by Nam Co, characteristics and seasonal differences of lake water temperature distribution were studied in a high altitude deep lake on the Tibetan Plateau, with in-situ monitoring data from different seasons. Then, seasonal variability of thermal stratification was emphatically analyzed. Results imply that in Nam Co, both the middle and eastern parts are frozen up in winter, completely mixed in spring and autumn, and steadily stratified in summer. Thus, Nam Co is a typical dimictic lake, and a holomictic lake at the same time. However, the two parts of Nam Co have unique characteristics in season variability of water temperature and thermal stratification respectively. In spring, temperature rises faster in the relatively shallow basin than that in the middle lake. Meanwhile, the date of summer stratification and autumn overturn is earlier in the shallow basin, in which water temperature is higher when circulated in autumn as well. By preliminary analysis, different topography under water and bathymetric distribution of the two basins probably contribute the most to the difference in the thermodynamic characteristic.