Phytoplankton, as primary producers in aquatic ecosystems, reflect the ecological structure and functional status of water bodies. As a major tributary of the Yangtze River and the largest river in the Poyang Lake Basin, the Ganjiang River is subject to the combined impacts of complex hydrological conditions and human activities, making phytoplankton highly sensitive to environmental changes. Based on hydroecological survey data of the mainstream of Ganjiang River (Ganzhou to Nanchang) between 2019 and 2024, combined with historical literature from 1980s, this study reveals the spatiotemporal distribution patterns and long-term succession characteristics of phytoplankton communities over nearly 40 years. Results indicate that 6 phyla and 84 species of phytoplankton were identified from 2019 to 2024, with Bacillariophyta being the dominant phylum. Spatially, the average total biomass of GJ11 (the south branch of the Ganjiang River) was the highest, while GJ5, GJ6, and GJ7 (the reservoir-controlled sections in the middle reaches) were lower. Seasonally, the highest biomass occurred in July 2020, and the lowest in January 2022. Redundancy analysis (RDA) revealed that CODMn, total phosphorus, ammonia nitrogen, total nitrogen, water temperature, transparency, and phosphate were the core environmental factors regulating phytoplankton community distribution in the mainstream of Ganjiang River, and the influence of river flow (hydrodynamic gradient) was non-negligible. In terms of long-term succession, the dominant phytoplankton groups in the mainstream of Ganjiang River from the 1980s to 2024 underwent a significant shift from " Bacillariophyta + Chlorophyta → cyanobacteria + Bacillariophyta → Bacillariophyta ", reflecting the response of Ganjiang River ecosystem to human activities (pollution, hydraulic engineering) and environmental governance. This study, through the cross-scale data integration of short-term continuous observations and long-term historical tracing, breaks through the limitations of short-term and localized in the previous studies on phytoplankton in the Ganjiang River. It accurately identifies the core driving factors of the spatiotemporal distribution of phytoplankton communities and reveals for the first time the succession patterns and ecological response mechanisms of dominant taxa over the past 40 years. The research results not only provide data support and a scientific basis for the aquatic ecological restoration and long-term management of the Ganjiang River Basin but also offer a typical case and methodological reference for studies on the long-term responses of riverine ecosystems to multiple disturbances.