Abstract: In June 2019 (flat water period), September (wet season) and February 2020 (dry season), 28 sampling sections were set up in the section from Sanhejian to Hongshantou in the middle reaches of Huaihe River to conduct phytoplankton and water quality environmental surveys. Based on the taxonomic data of phytoplankton community structure and morphologically based function group (MBFG) in the middle reaches of Huaihe River, the phytoplankton biological integrity index (P-IBI) evaluation system was constructed for the three hydrological periods, and the ecological health was evaluated. The comprehensive trophic status index was used as the classification standard to determine the reference section and the damaged section, and the distribution range test, correlation test and discrimination ability analysis of the candidate indicators were carried out to screen out the core parameters of P-IBI in each hydrological period, and the ratio method was used to determine the grading evaluation standard, and the water ecological health evaluation of the middle reaches of the Huaihe River was evaluated. The results showed that a total of 128 species and 8 phyla of phytoplankton were identified in the middle reaches of Huaihe River, and 7 functional groups were detected in the three hydrological periods in the phytoplankton morphological functional group classification, and the dominant phytoplankton functional groups were III+IV+V+VI (flat water period), III+V+VI+VII (wet season), and I+VI+VII (dry season). The water ecological health grades of “sub-health”, “moderate disturbance” and “mild disturbance” were respectively “sub-healthy”, “moderate disturbance” and “mild disturbance” during the normal water period, wet water period and dry water period, respectively, and 75.00% of the health status of the survey section was at the level of “slight disturbance” or above, indicating that the overall water ecological restoration effect was good, and the water ecological health status showed a distribution pattern that the downstream was better than the upstream, and the lower part of the sluice was better than the upper sluice. The evaluation results well reflect the water ecological health status of different hydrological periods and river sections in the middle reaches of Huaihe River, which can provide data support and theoretical basis for the governance and water ecological restoration of Huaihe River.