Climate warming and atmospheric deposition have become the main environmental stressors for alpine lakes, however, the long-term response of biotic community in alpine lakes has been predominantly derived from algae rather than from biota at higher trophic levels (e.g., zooplankton). Here, a deep-water alpine lake, i.e., Wodi Co, was selected for a paleolimnological survey through multi-proxy sediment analyses (total nitrogen (TN), total phosphorus (TP), chlorophyll-a (Chl.a), stable isotopes of nitrogen, etc.) in combination with published records on regional climate change. With the historical reconstruction on the changes in lake and catchment environment, cladoceran remains were analyzed for taxonomic composition and production in quantifying the temporal pattern of community responses and environmental drivers in this alpine lake over the past two centuries. The time series showed that the nutrient level (e.g., TN) and primary productivity (i.e., Chl.a) generally showed a temporal trend of continuous increase. Correlation analysis showed that atmospheric nitrogen deposition and exogenous organic matter input were the main factors for the increase in TN, while both climate warming and nutrient enrichment led to a continuous increase of lake primary production. Since the 1960s there was an obvious warming of regional climate, meanwhile there was an accelerating increase in both lake nutrient level and Chl.a concentration. Regarding the sediment cladoceran assemblages, the planktonic species was found to be the dominant taxa such as Daphnia longispina. The relative abundance of D. longispina was relatively stable (40.83%±8.02%) before 1900 AD, but it decreased noticeably from 1948 to 1965 before it increased again and became the dominant species more recently. The Ordination analysis showed that, climate change, variation of nutrient level (TN) and Chl.a concentration were the main driving factors for the cladoceran community change before 1960s, thereafter, lake-water nutrition level (TN) and primary productivity became the main factors in driving cladoceran community shifts. In all, this study reveals the long-term effects of regional climate, atmospheric deposition and catchment surface processes on zooplankton communities in alpine lake and its stronger coupling with algae more recently. These findings can help evaluate key processes in driving ecological and environmental changes, and predict the future trajectories of their responses in alpine lakes under global change.