From January 2010 to March 2014, detailed depth profiles of water temperature, dissolved oxygen (DO), and chromophoric dissolved organic matter (CDOM) were collected at three sites in Lake Qiandaohu, a large, deep subtropical reservoir in China. Additionally, we assessed the changes in DO stratification over the past 61 years (1953-2013) based on our empirical models and long-term air temperature and transparency data. The DO concentration never fell below 2 mg/L, the critical value for anoxia, and the DO depth profiles were closely linked to the water temperature depth profiles. In the stable stratification period in summer and autumn, the significant increase in CDOM in the metalimnion explained the decrease in DO due to the oxygen consumed by CDOM. Well-developed oxygen stratification was detected at the three sites in spring, summer and autumn and was associated with thermal stratification. Oxycline depth was significantly negatively correlated with daily air temperature and thermocline thickness but significantly positively correlated with thermocline depth during the stratification weakness period (July-February). However, there were no significant correlations among these parameters during the stratification formation period (March-June). The increase of 1.67 °C in yearly average daily air temperature between 1980 and 2013 and the decrease of 0.78 m in Secchi disk depth caused a decrease of 1.65 m and 2.78 m in oxycline depth, respectively, facilitating oxygen stratification and decreasing water quality. Therefore, climate warming has had a substantial effect on water quality through changing the DO regime in Lake Qiandaohu.