In order to understand the thermal stratification, the characteristics of the water quality and the application of water-lifting aerator system in the deep reservoir, water temperature, dissolved oxygen, pH, chlorophyll-a, nutrient and dissolved organic carbon(DOC) were monitored in a whole year. The results showed that Heihe Reservoir belonged to single hybrid mode, and the natural thermal stratification period was from March to October. The thermal stratification led water quality stratifications. The chlorophyll-a, total phosphorus, total nitrogen, ammonium nitrogen and DOC average concentrations were 2.21 μg/L, 0.022 mg/L, 1.32 mg/L, 0.20 mg/L and 2.93 mg/L, respectively, which showed that Heihe Reservoir was mesotrophic. In the thermal stratification period, the dissolved oxygen in the underlying water ranged from 0 mg/L to 7.9 mg/L, with an average of 2.9 mg/L, and the ratio of N/P was between 41 and 100, which showed that Heihe Reservoir had a seasonal hypoxia, with high nutrient concentrations. In the end of natural thermal stratification period, the application of water-lifting aerator technology can not only improve the bottom anaerobic/anoxic environment, and reduce the release of endogenous pollutants and the proliferation of algae, but also enhance the water mixture.