It is of great scientific significance to study feature differences of bacterial community structure between sediment and water in the plateau lakes for water ecological management and protection. We selected 19 objective lakes in the central and eastern of the Qinghai-Tibet Plateau, collected the samples of sediment and water, and analyzed differences of bacterial community structures, spatial distributions, co-occurrence network patterns, community assembly processes between sediment and water in lakes based on high-throughput sequencing and statistical analysis. The results showed that alpha diversity indices of bacterial community in sediment, including Chao1, Shannon diversity, Faith's phylogenetic diversity and Pielou's evenness indices, were significantly higher than those in water. Dominant phylum in both sediment and water was Proteobacteria with the relative abundances of 45.33% and 41.77%, respectively, while bacterial community structures in water presented stronger spatial heterogeneity than in sediment. The results of principal coordinate analysis and similarity analysis showed that there were significant differences in bacterial community composition between sediment and water. Altitude and Latitude were the most important environmental drivers in shaping bacterial community compositions in sediment and water. Both sediment and water bacterial community had distance-decay patterns, while bacterial spatial turnover rate in sediment was lower than that in water. The co-occurrence network complexity and stability of bacterial community in sediment were higher than those in water. The mean value of normalized stochasticity ratios in sediment and water bacterial were 0.24 and 0.72, indicating deterministic process played a key role in sediment bacterial community assembly processes, whereas water bacterial community assembly processes was predominant by stochastic process. These findings about bacterial community features, spatial patterns, stability of co-occurrence networks, assembly processes, and their differences of bacterial between lake sediment and water in the Qinghai-Tibet Plateau would provide the scientific support for in-depth understanding mechanisms of bacterial diversity and composition formation in plateau lakes.