This study aimed to examine the distribution characteristics of phytoplankton communities in typical lakes in Inner Mongolia and their relationships with environmental factors, focusing on the effects of key factors such as nutrient levels, salinity, and water temperature on phytoplankton community structure. Using multivariate statistical analysis, the community composition, dominant taxa, and their interactions with environmental factors were analyzed across 79 sampling sites distributed among 20 lakes in these six regions. The results indicated significant differences in community structure along a nutrient gradient: Cyanobacteria predominated in eutrophic lakes, whereas Chlorophyta and Bacillariophyta were more common in saline lakes. Nutrient concentrations, particularly total nitrogen and phosphorus, were the main drivers of phytoplankton community changes, leading to frequent cyanobacterial blooms in eutrophic lakes. Salinity significantly regulated phytoplankton diversity, especially in arid and semi-arid regions. Lake eutrophication and phytoplankton proliferation not only altered the community structure but also affected ecosystem stability and function. Certain integrated management strategies, including pollution control, water allocation, and ecological restoration, can effectively mitigate eutrophication-related ecological issues. This study provides essential scientific insights into lake ecological management.