In recent years, the Yitong River in Changchun City has been polluted by human activities to a certain extent, and therefore, it is necessary to monitor its water quality. Phytoplankton are sensitive to environmental changes and are an ideal biological indicator for environmental monitoring. This study studied the phytoplankton distribution in eight sampling sites of the Changchun section of the Yitong River from April to September 2019. The aim was to investigate the relationships between phytoplankton community structure’s temporal and spatial distribution characteristics and water quality in the Changchun section of the Yitong River. Environmental factors such as the total nitrogen (TN), total phosphorus (TP), water temperature (WT), ammonia nitrogen (NH₃-N), chemical oxygen demand (COD_Cr), permanganate index (COD_Mn), and chl-a were measured and assessed. The results identified 161 species of phytoplankton belonging to eight phyla among eight sampling sites of the Changchun section of the Yitong River, including 67 species of Chlorophyta, 11 species of Cyanobacteria, and 51 species of Bacillariophyta. The percentage of Cyanobacteria phytoplankton abundance in the urban area was higher than that in the reservoir and the wet regions. From the temporal perspective, the total phytoplankton density and biomass peaked in summer, with the highest values recorded in June, followed by July. The study showed that TN, TP, and chl-a were the main environmental factors affecting the phytoplankton community structure in the Changchun section of the Yitong River.