Abstract: Evaluation of water ecological health status helps to judge the effectiveness of water ecological restoration, which is an effective means of water environment management. In order to explore the water ecological health status of Cyprinus carpio and Leiocassis longirostris national aquatic germplasm resources reserve in Huaihe River, according to the survey results of phytoplankton community structure in 2020 and combined with the morphological functional group classification, we constructed the ecological health evaluation system of the reserve based on the biological integrity index of phytoplankton. Besides, we carried out the Mann-Whitney non-parametric test and correlation analysis of the candidate parameters to determine the final evaluation parameters, and used the ratio method to determine the grading evaluation standard for the evaluation of the health status of the reserve water. The results show that the evolution trend of dominant functional groups of phytoplankton was III+IV+V (Spring)→III+IV+V+VI (Summer)→V+VI (Autumn)→IV+V+VI (Winter). Except that the dominant functional groups in the core area were III+ IV+V+VI, the dominant functional groups of the experimental area, the Guo river and the Huaihe River were III+IV+V+VI. 68.06% of the sampling sites in the reserve were evaluated as "average" or above, indicating that the overall water ecological health status was good. Specifically, the temporal pattern of winter was better than autumn, followed by summer, and the worst was in spring; the spatial pattern of Huaihe River mainstream was better than Guohe River, and the experimental area was better than the core area.