In order to assess the aquatic ecosystem health in Yongjiang River, 13 sites from were sampled annually for density of individual phytoplankton species and community composition. Box-plots and Pearson correlation of 21 pre-selected metrics were then analyzed based on annual sampling and statistics data of the phytoplankton community. These metrics represent the characteristics of the phytoplankton community. Five of them were then used independently to evaluate the health of the aquatic ecosystem. It was found that the aquatic ecosystems’ health at all sampling sections in Yongjiang River was good. After calculating P-IBI values at each section and then comparing the values with the corresponding evaluation criteria, we found that the health at the upstream sections was better than the downstream sections.