As a major source of water supply for cities, deep reservoirs usually form thermal stratification due to the uneven vertical heat distribution. Thermal stratification can hinder the vertical water exchange, thus cause water quality stratification. In winter, the water mixing caused by the"turnover"of a reservoir leads to the deterioration of overall water quality. With the application of thermal stratification index, the reservoir thermal stratification stability can be objectively and directly expressed. Integrated with the annual changes of reservoir temperature, water renewal rate and water quality parameters (dissolved oxygen, pH, total phosphorous, ammonia nitrogen), this paper studied the thermal stratification conditions of Heihe Reservoir, Shanxi Province, in 2008-2010. Studies showed that the formation of the thermal stratification could directly deteriorate the water quality and particularly accelerate the consumption of dissolved oxygen, in the bottom water. Although annual changes of thermal stratification are mainly controlled by the temperature, at certain periods the higher water renewal rate can weaken the thermal stratification to some extent, and mitigate the deterioration of the bottom water quality. The results show that during the periods of the most stable thermal stratification managers of the most serious deteriorating water quality reservoirs can manually adjust the water renewal rate to weaken the thermal stratification; this is a valuable mechanism in safeguarding the water quality.