In order to understand the seasonal changes of niche and community structure stability of dominant species of phytoplankton under the coexistence of multiple water sources (local reservoir water, Yangtze River water, and Yellow River water) in the Xiashan Reservoir, the strategic water source of the Shandong Province, this study conducted the quarterly sampling of phytoplankton at 10 representative sampling sites of Xiashan Reservoir in 2019. Niche breadth, niche overlap, variance ratio method, Chi-square test and association coefficient were used to analyze the niche and interspecific associations of dominant species. The results showed that a total of 7 phyla, 78 genera and 95 species of phytoplankton were identified in Xiashan Reservoir, of which 4 phyla, 12 genera and 12 species were the dominant species. Phytoplankton in all seasons were dominated by Cyanobacteria except for spring. Limnothrix redekei, Planktothrix agardhii and Pseudanabaena moniliformis were the dominant species throughout the year. The diversity index showed a more consistent trend, with higher phytoplankton diversity in spring and the lowest diversity in summer. The niche breadths of dominant species varied greatly, ranging from 0.526 to 2.224, with the maximum and minimum values in Pseudanabaena moniliformis in autumn and Chromulina sp. in spring, respectively. Pseudanabaena moniliformis had the largest niche breadth and strong ability to adapt to diverse habitats in many seasons. Niche overlap analysis showed that Pseudanabaena moniliformis and other dominant cyanobacteria had the largest niche overlap values in different seasons, and it was the only dominant cyanobacteria that declined in spring, summer and autumn but developed rapidly in winter. The overall correlation difference of dominant species in four quarter was more obvious, and the community structure was unstable. The Chi-square test showed that 76% of the species pairs had significant positive associations, forming a stable succession pattern that community structure was dominated by Pseudanabaena moniliformis, sharing the same resources and space with other dominant cyanobacteria. In addition to the possible algal blooms in summer and autumn, reservoir management and water transfer department should also pay close attention to the abnormal proliferation of some algae in low temperature seasons, especially the Pseudanabaena moniliformis in winter. This research can provide theoretical basis and data support for algal bloom early warning and multi-source dispatching of related reservoirs in Jiaodong Water Transfer Project.