Chlorophyll-a is an important indicator of primary productivity in lake ecosystems, and its concentration changes reflect the nutritional status and ecological health of lakes. Based on water quality and environmental data from Lake Chagannaoer between 2011 and 2024, this study used correlation and redundancy analysis to reveal the interannual and seasonal variation characteristics of chlorophyll-a concentration and its key driving factors. The results showed that between 2011 and 2024, the interannual variation of chlorophyll-a concentration in Lake Chagannaoer was stable, mainly regulated by hydrological conditions, nutrient inputs, and human activities. Seasonally, chlorophyll-a concentration follows the pattern of summer＞winter＞autumn＞spring. In spring, water dilution led to a decrease in chlorophyll-a concentration, while in summer, the rise in temperature promoted phytoplankton proliferation. Autumn cooling inhibited reproduction, and winter freezing led to the migration of nutrients into the water, with photosynthesis under the ice maintaining relatively high chlorophyll-a concentrations. The study further found that in spring and autumn, chlorophyll-a concentration was positively correlated with total nitrogen and negatively correlated with total phosphorus; whereas in summer and winter, chlorophyll-a concentration was negatively correlated with total nitrogen and positively correlated with total phosphorus, reflecting the seasonal impact of nutrient changes on phytoplankton growth. Redundancy analysis further indicated that the seasonal variation of chlorophyll-a concentration was influenced not only by the current season's climate and environmental factors but also by the interactions between consecutive seasons, creating cross-seasonal chain effects. Future research should focus on inter-seasonal relationships and environmental effects to further uncover the complexity of lake ecosystems, providing scientific evidence for lake management and conservation.