Biodiversity and the mechanisms of community assembly are research hotspots. Phytoplankton， as primary producers in aquatic ecosystems， have important aquatic ecological functions， and there are few related studies at the level of the Yangtze River basin. In this study， we used environmental DNA macro-barcoding technology to investigate the community composition and construction mechanism of phytoplanktonic diatoms and green algae in the Yangtze River during the dry season.The results showed that a total of 389 operational taxonomic units （OTUs） belonging to 62 families and 101 genera were detected in the whole Yangtze River basin， with more green algae. A total of 378， 322 and 318 OTUs were detected in the upstream， midstream and downstream of the Yangtze River， respectively， and the species diversity in the lower and upper reaches of the Yangtze River was relatively high， with the median value of the Shannon-Wiener index exceeding 2.0. Mantel's test showed that the upper reaches of the Yangtze River were significantly correlated with pH （P<0.05）； the middle reaches of the Yangtze River were highly significant correlated with total organic carbon （P<0.01）， and the middle reaches of the Yangtze River were significantly correlated with electrical conductivity （P<0.05）. downstream diatom communities were highly significantly correlated with dissolved oxygen， permanganate index and fluoride ion （P<0.01）.Redundancy analyses indicated that total nitrogen was the strongest explanation for diatom communities throughout the watershed， followed by conductivity. In addition， neutral and null model analyses indicated that community construction of diatoms and green algae in the Yangtze River was mainly dominated by stochastic processes； the community composition showed an obvious distance decay pattern， and the distance decay phenomenon was increasingly significant from upstream to downstream.