Microorganisms are important organic components of lake ecosystems. Understanding the differences in bacterial community structures, environmental driving factors and their community assembly processes in different periods in the lakes on the Qinghai-Tibet Plateau (QTP) has significant guiding role for water ecological management of the plateau lakes. Water samples were collected from five lakes on the northeastern of the QTP in June and December in 2020 for investigating the differences of community structures, environmental driving factors as well as the contributions of neutral processes, deterministic processes, and stochastic processes of bacterial communities in the plateau lakes between non-freezing and freezing periods using the high throughput sequencing, statistical analysis, and the model analysis. Results show that: (1) The Chao 1 richness index, Simpson, and Shannon diversity indices of bacterial communities were lower in non-freezing periods than those in freezing periods. Spearman correlation analysis revealed that water temperature and altitude were the most important factors in influencing Chao 1 richness index and diversity indices in non-freezing periods, while total nitrogen had a significant relationship with bacterial Chao 1 richness index and diversity indices in freezing periods. (2) The predominant phylum was Proteobacteria both in non-freezing and freezing periods. High average relative abundances of Bacteroidetes, Actinobacteria and Firmicutes were observed in non-freezing periods. Additionally, the results of principal coordinate analysis (PCoA) and similarity analysis showed that there were significant differences in the bacterial community compositions in non-freezing and freezing periods. (3) Results of redundancy analysis indicated that driving factors of bacterial community compositions were also different between non-freezing and freezing periods, which were in the order of total nitrogen>latitude>total dissolved solid>longitude>dissolved organic carbon in non-freezing periods and altitude>dissolved oxygen>dissolved organic carbon>pH in freezing periods, respectively. (4) Variations of bacterial communities were controlled by neutral process which was stronger in freezing periods than that in non-freezing periods and a higher dispersal rate was found in freezing periods than that in non-freezing periods (freezing periods: 0.289; non-freezing periods: 0.130) which reflected that the dispersal ability of bacterial species was higher in freezing periods than that in non-freezing periods. Dispersal limitation of stochastic processes shown to be a dominating process in the assembly of the bacterial communities both in non-freezing (contribution=54.74%) and freezing (contribution=55.56%) periods. Our study has analyzed the characteristics and driving mechanisms of bacterial communities in the plateau lakes in two different periods and will provide guidance for protection and management of the water resources in the plateau and basis for understanding bacterial community assembly processes.