To discuss the impact of the daily minimum temperature on phytoplankton community structure, the long-term relations of phytoplankton community structure with both meteorological elements and physicochemical factors in Lake Pyhäjärvi have been studied by using non-metric multidimensional scaling method to analyze the detected data in summers during 1987-2013. Results from the fitted data suggested that warming trend in Lake Pyhäjärvi is significant in summer, especially the trend of daily minimum temperature. In summer, phytoplankton community structure is mainly influenced by meteorological elements, among which daily minimum temperature is the most significant. This may because many physiological processes of phytoplankton have significant circadian rhythm. The increase of daily minimum temperature can enhance the nighttime respiration and absorption of nutrients, so as to influence the growth and proliferation rates. Adaption of temperature ranges for different species is inconsistent, so the increase of daily minimum temperature is also likely to influence the community structure of phytoplankton.