Beta diversity can be a result of unique structuring processes:turnover (caused by species replacement from site to site) and nestedness (caused by species losses in nested subsets). Based on the Baselga proposed framework for beta diversity partitioning measures, the total beta diversity and its components of mollusk in the lakes of Yunnan Plateau were studied. According to multiple-site calculating methods, the results showed that the total beta diversity of the mollusk is 0.8903 (Sørensen index) and 0.9419 (Jaccard index). The turnover component accounted for 80.93% (Sørensen index) or 88.92% (Jaccard index) of the total beta diversity, respectively. The total beta diversity of Lamellibranchia is greater than that of Gastropoda, across basins from the highest to the lowest is that of Jinshajiang, Lancangjiang, Nanpanjiang and Yuanjiang, and total beta diversity of deep lakes is greater than that of shallow lakes. The proportion of beta diversity attributed to turnover of Lamellibranchia is higher than that of Gastropoda, across basins from the highest to the lowest is that of Yuanjiang, Nanpanjiang, Lancangjiang and Jinshajiang, and that of deep lakes is greater than that of shallow lakes. According to the pairwise measuring method, the distribution of total beta diversity and its turnover and nestedness components varied depend on lakes pair. The distribution pattern of turnover was uniform, and nestedness presented a unimodal model distribution. The maximum value of the turnover is 1, and the minimum value is 0, indicating that there are complete turnover and complete nestedness pattern between lakes. So, results suggest that mollusk conservation should not be focused solely on protecting lakes with the highest species richness, but should consider a variety of lakes across a region.