Objective: Environmental DNA (eDNA) technology is an emerging tool for the biological monitoring of aquatic ecosystems. It enables an efficient molecular analysis of the structural characteristics of aquatic communities by capturing DNA fragments freely present in water. This study focuses on the following objectives: (1) analyzing the spatial distribution patterns of winter zooplankton diversity and community composition in the Xiangjiaba section of the lower Jinsha River; (2) exploring the assembly processes and driving factors of winter zooplankton communities; (3) assessing the potential impacts of hydropower development on zooplankton diversity in this section during winter; and (4) identifying key environmental factors affecting zooplankton community structure and elucidating the regulatory mechanisms involved. Methods: This study applied eDNA metabarcoding to investigate winter zooplankton communities in the Xiangjiaba section of the lower Jinsha River. Species, phylogenetic, and functional diversity indices were calculated to evaluate the α-diversity. β-diversity was partitioned into species turnover and nestedness components. Community composition variations were assessed by applying Bray-Curtis distance, principal coordinates analysis (PCoA), and permutational multivariate analysis of variance (PerMANOVA). Key taxa were identified using linear discriminant analysis effect size (LEfSe). Co-occurrence networks were constructed utilizing sparse correlations for compositional data (SparCC) to evaluate community structure and stability. Random forest models were employed to identify crucial environmental drivers shaping zooplankton diversity patterns. Results: The Xiangjiaba Hydropower Station significantly impacted the α-diversity of winter zooplankton in the lower Jinsha River. Specifically, the downstream area of the mainstream river exhibited markedly higher Chao1 richness (Chao1) and phylogenetic diversity than the upstream regions. Additionally, both indices gradually declined toward the dam, suggesting a "homogenization effect" caused by reservoir regulation. Regarding functional traits, functional richness (FRic) and functional divergence (FDiv) were markedly greater in the tributaries than in the mainstream, reflecting a greater ecological niche differentiation in less-regulated habitats. The composition of dominant zooplankton groups varied across different water body types. Protozoans dominated the downstream region of the mainstream, whereas copepods were predominant in the upstream tributaries. The upstream region of the mainstream exhibited moderate protozoan abundance levels but lacked a single dominant group. Co-occurrence network analysis revealed that the downstream area of the mainstream had a more complex and robust network structure, with higher connectivity and lower vulnerability, indicating enhanced community stability. At the river section scale, the β-diversity of the winter zooplankton was primarily driven by species turnover, with species replacement being the primary community assembly process. Tributaries exhibited significantly enhanced β-diversity compared to the mainstream, largely due to spatial isolation and heterogeneous environmental conditions. The upstream area of the mainstream, functioning as a transition zone between the tributaries and downstream, demonstrated greater environmental homogenization and reduced community dissimilarity. Conclusions: Hydrological dynamics (e.g., water depth, flow velocity, and water level fluctuations) and water quality (e.g., temperature and turbidity) are the main environmental factors influencing α-diversity patterns of winter zooplankton. Variations in nutrient levels (e.g., chlorophyll a) and water quality (e.g., conductivity and water temperature) are the key drivers of β-diversity and its components, particularly species turnover. These findings suggest that developing hydropower stations and associated environmental changes notably influence zooplankton community structure and assembly processes. Tributary inflow and dam-induced habitat modifications are critical in shaping spatial biodiversity patterns in regulated river systems.