Abstract: In order to fully and accurately evaluate the characteristics of phytoplankton community structure and its relationship with environmental factors in the middle and late periods of Chinese mitten crab (Eriocheir sinensis) pond culture, we had monitored the water quality indexes and phytoplankton community of aquaculture crab ponds from June to October 2022, and identified the phytoplankton community by artificial microscopy and high-throughput sequencing based on morphological and metagenomics methods. Then we discussed the relationship between dominant phytoplankton species and environmental factors. The results show that 65 species in four phyla were identified by artificial microscopy, and 1 463 species by metagenomic data analysis, in which the dominant species identified by artificial microscopy were Microcystis flos-aquae, Aphanocapsa elachista and Skeletonema costatum, and the dominant species identified by metagenomic data analysis were Aphanizomenon flos-aquae and M. aeruginosa. The diversity index calculated by manual microscopy was generally lower than that of metagenomic results. Dissolved oxygen, chlorophyll a, total nitrogen and ammonia nitrogen were the key environmental factors affecting phytoplankton community structure. It is suggested to simutaneously use artificial microscopy and high-throughput sequencing methods to analyze phytoplankton community structure in aquacultural water, so as to evaluate the characteristics of phytoplankton community structure and its relationship with environmental factors in aquaculture ecosystems more comprehensively and accurately.