Studies about changes of zooplankton (e.g., Cladoceran) community and biomass, as well as the carbon sources of food web in alpine lake will deepen the understanding of lake ecosystem response to regional climatic and environmental changes. In this study, multi-index analysis of sediment core was carried out in Lake Taiji, an alpine lake in Northwest Yunnan, including the subfossil assemblage of cladoceran, the stable carbon isotope (δ¹³C) of Daphnia ephippia and chironomid headshield, and geochemical indicators (total nitrogen (TN), total phosphorus (TP), δ¹⁵N and C/N etc.), in order to understand the response pattern of cladoceran to regional environmental change and the characteristic of carbon sources change in the food web in the alpine lake during the past 200 years. Changes of TN suggested that the lake nutrient level was continue increasing in the past 200 years. Analysis suggested that exogenous inputs from the catchment and atmospheric nitrogen deposition were the main factors which driving the nutrient enrichment, regional warming and nutrient enrichment also promoted the enhancing of lake primary productivity (chlorophyll-a). Cladoceran community was dominated by littoral species Alona affinis and the facultative planktonic species Chydorus sphaericus. Before 1970s, there was no significant change of cladoceran community, after then, the relative abundance of C. sphaericus was decreased, associated with increase of A. affinis. Redundancy analysis shown that the annual average temperature and primary productivity (chlorophyll-a) were the main driving factors for the succession of cladoceran community in the past 200 years. For the stable carbon isotope values (δ¹³C), the δ¹³C of Daphnia ephippia was negative from 1860s to 1940s, probably attributed by the inputs of exogenous material, which supported by the lower lake primary productivity and higher C/N in this period. From 1940s to 2020s, the δ¹³C of Daphnia ephippia was significantly enriched, which may be affected by the enhanced primary productivity as well as the increase abundance of benthic algae. The δ¹³C value of chironomid headshell shown minimal change in the past 200 years, only had a negative trend from 1990s to 2010s, probably related to the increase inputs of terrestrial debris which driving by the increase precipitation in this period. Discrepancy in δ¹³C values between the Daphnia ephippia and chironomid headshield, indicated that there were different organic carbon composition in the planktonic and littoral zone, and affected by the changes of lake primary productivity and terrestrial inputs. Those findings reveal that regional climate change and catchment inputs changed the productivity and carbon source composition of aquatic food web in alpine lake, and ultimately affected the cladoceran community composition and stable carbon isotope values of aquatic organisms.