Dam construction changes the migration and transformation of biogenic elements and inevitably affecting the structure and function of river ecosystem. To explore the phytoplankton community characteristic and its driving factors along cascade reservoirs, we investigated the phytoplankton communities and environmental factors in wet seasons of 2016, 2018 and 2021, and dry seasons of 2018 and 2021 respectively, in a cascade river, the Lancang River. This study focused on the comparison of phytoplankton communities between natural riverine and reservoirs in wet seasons. The widely used generalized additive model (GAM) was applied to analyzed the complex relationships between phytoplankton and key environmental factors. The results showed that phytoplankton biomass in wet seasons was significantly higher than that in dry seasons. Phytoplankton community was dominated by diatoms in the upper reaches, and chlorophyta and cyanobacteria in the middle and lower reaches. Based on the GAM model, nutrients and hydraulic retention time (HRT) were the dominant environmental factors which contributed to phytoplankton biomass differences between upstream and downstream. Total phosphorus (TP), water temperature and HRT were the key environmental factors affecting the Shannon-Wiener diversity index. TP and ammonia nitrogen were the crucial environmental factors affecting the Margalef species richness index. These findings can help to deepen our understanding about the water ecological environment effects of cascade reservoirs.