Lakes in cold climatic zones own unique biological community successions and reciprocal feedbacks between species during frozen period. As typical lakes in the Inner Mongolia section of the Yellow River Basin, long frozen period provides a natural platform for the study of bacterial and cyanobacterial interactions under frozen conditions. Clarifying such interactions in different lakes can gain a deeper understanding of the functioning and dynamics of the aquatic ecosystems of the lakes under frozen conditions. To elucidate the bacteria-algae interactions of different lakes, this paper collected subglacial water samples from Lake Ulansuhai, Lake Nanhai and Lake Daihai. Bacteria and cyanobacteria and their community structure and relationships between frozen period were investigated using metagenomic sequencing molecular biology technology, redundancy analyses, Mantel test analyses and network analysis models. Results demonstrated that the four major phyla in the three lakes were Proteobacteria, Bacteroidetes, Actinobacteria and Cyanobacteria during the frozen period. The three lakes have significant differences in bacterial and cyanobacterial community composition at the genus level, exhibiting strong relationship with environmental conditions. It is noteworthy that salinity has a significant impact on the microbial composition in Lake Daihai, while ammonia nitrogen concentration imposes great impact on Lake Nanhai. The analysis of the bacteria-cyanobacteria network revealed that more complicated relationship in Lake Nanhai than the other two lakes. More bacteria and algae had competitive antagonistic relationships in Lake Daihai, which is known for its high salinity. Meanwhile, the bacteria-cyanobacteria networks in Lake Daihai and Lake Ulansuhai exhibited higher stability than those in Lake Nanhai. In order to better understand the abiotic factors affecting the co-evolution of bacteria and cyanobacteria, the aim of this paper to sort out the abiotic factors of dominant bacteria and cyanobacteria in the aforementioned three different types of lakes. It also analyzes the significant synergistic relationship between bacteria and cyanobacteria in the three lakes. Finally, it serves as a reference for anticipating and managing lake water issues during frozen period.