Currently, studies on the assessment of ecological integrity mainly focus on the development of the fish or benthic index of biotic integrity for rivers and lakes, and there are few studies on phytoplankton in reservoirs. Therefore, the phytoplankton communities were investigated three times in the Nanwan Reservoir, a water supply reservoir in the Huaihe River Basin in 2016. An ecological integrity assessment was conducted based on the phytoplankton biological integrity using factor analysis. The results showed that the number of phytoplankton species in the three investigations changed marginally, but there was a clear seasonal difference among the species. The density of phytoplankton was the highest in September and the lowest in March, but the biomass was the highest in March and the lowest in September. The factor analysis was used to further analyze and assess the ecological status. Four common factors were identified in the factor analysis. Among them, factor 1 characterizes the characteristics and ability of the community to resist pollution, factor 2 characterizes the diversity of the community, factor 3 characterizes the richness of the community, and factor 4 characterizes the eutrophication of the water body. The factor scores showed obvious difference in different months. The ecological condition in March was the best. Further, from the spatial point of view, the water ecological condition of the area with high population density was very poor. The factor score better reflects the relative size of the water ecological status of the reservoir at different times and locations. This indicates that the assessment of biological integrity based on factor analysis is suitable for the Nanwan Reservoir and can be applied to the ecological assessment of other water bodies.