Based on the community change of overwintering cyanobacteria, this study aimed to elucidate ecological changes in different lakes. A sampling program was conducted at 10 sampling sites in Lake Daihai, Lake Wuliangsuhai, and Lake Nanhai in January and July 2022, with samples from the upper water and sediment. These samples were used to investigate the community structure, abundance variations, and diversity of cyanobacteria in various types of lakes in the Inner Mongolia lake region during both the ice-covered and non-ice-covered periods. The results showed large variation in the abundance and diversity of cyanobacteria between the ice-covered and non-ice-covered periods of lakes, providing a good explanation for the ecological changes. During the non-ice-covered period, the abundance of cyanobacteria in Lake Wuliangsuhai and Lake Nanhai was significantly higher than that during the ice-covered period. Conversely, in Lake Daihai, the abundance of cyanobacteria in water was significantly higher during the ice-covered period than that during the non-ice-covered period, attributed to the unique water quality of the lake, and the abundance of cyanobacteria in the sediment during the non-ice-covered period was significantly higher than that during the ice-covered period. Additionally, the ecological niche widths of the dominant genera in different lakes varied across periods. Specifically, the dominant cyanobacteria in Lake Daihai and Lake Nanhai were generally able to utilize a diverse range of resources during both the non-ice-covered and ice-covered periods, whereas the dominant cyanobacteria in Lake Wuliangsuhai had fewer resources readily available to them. Based on neutral modeling and redundancy analysis, it is clear that during the non-ice-covered period, the water bodies and sediments of Lake Wuliangsuhai and Lake Nanhai were significantly influenced by stochastic processes. In contrast, the sediments of Lake Daihai and the water of Lake Nanhai were more constrained by environmental factors. Additionally, there were seasonal variations in the composition and structure of cyanobacterial communities in cold-region lakes, with the main driving factors of water temperature, total nitrogen, ammonia nitrogen and pH. This study can serve as a valuable reference for the protection and management of lake ecology in cold regions.