The seasonal shift in the homogeneity of the periphytic protozoan fauna was studied based on a four-season baseline survey in the coastal waters of the Yellow Sea, northern China. Samples were collected using glass microscope slides as an artificial substratum at a depth of 2 m after the immersion time of 14 days during each of the four seasons (winter, spring, summer, and autumn, 2017). The protozoan fauna showed a clear seasonal shift in species composition and a significant variation in homogeneity in terms of both compositional and community structure during four seasons. The dispersion measures and β-diversity index represented an increase in the trend from spring to winter. These findings suggest that the homogeneity of the periphytic protozoan fauna was subject to a significant variability shaped mainly by species composition during a four-season cycle in marine ecosystems.