Based on the seasonal survey results on the current status of phytoplankton at six sampling sites in the Jiangsu section of the Yangtze River from July 2016 to April 2017, and through screening parameters on the basis of MBFG taxonomy of phytoplankton, the phytoplankton index of biotic integrity(P-IBI)was constructed. The sampling point with the least human interference was selected as the reference point, and the candidate parameters were screened through discrimination ability and correlation analysis to obtain 9 core parameters for P-IBI construction. Using the ratio method to unify the parameter dimension and determine the grading evaluation standard, the water ecological health of the Jiangsu section of the Yangtze River was evaluated. The results showed that: P-IBI changes in the shape of "N" in space. The sections in Zhenjiang and Nantong have higher scores, while those in Jiangning, Qixia and Jiangyin have lower scores. P-IBI was significantly negatively correlated with water temperature and COD_Mn, and positively correlated with transparency and dissolved oxygen(DO). The growth and reproduction of Ⅲ functional groups have an important impact on P-IBI, and their large-scale reproduction will lead to deterioration of aquatic ecosystem conditions.