In this paper, two trophic lakes: Lake Taihu and Lake Yanghe, and three alpine lakes: Lake Qinghai, Lake Keluke, and Lake Tuosu, were investigated to discover the connections between environmental factors and the phytoplankton community in lakes with differences in trophic levels and climatic conditions. Three seasonal data, including water quality and phytoplankton, were collected from the five lakes. The results demonstrated clear differences in water parameters and phytoplankton compositions in different lakes. The phytoplankton was dominated by Bacillariophyta, followed by Cyanobacteria and Chlorophyta in Lake Qinghai, Lake Keluke, and Lake Tuosu. It was dominated by Cyanobacteria (followed by Chlorophyta and Bacillariophyta in Lake Yanghe) and Cyanobacteria (followed by Chlorophyta and Cryptophyta in Lake Taihu). The temperature was an essential factor favoring the growth of Cyanobacteria, Chlorophyta, and Bacillariophyta, especially Cyanobacteria and Chlorophyta. The pH had significantly negative relationships with Cyanobacteria, Chlorophyta, and Bacillariophyta. Particularly, a high pH might be a strong and negative factor for phytoplankton growth in alpine lakes. A high salinity was also an adverse factor for phytoplankton. Those results could provide fundamental information about the phytoplankton community and their correlated factors in the alpine lakes of the Tibetan Plateau, contributing to the protection and management of alpine lakes.