Exploring the response of the diversity of phytoplankton species and functional groups to environmental variables is extremely important in maintaining biodiversity in aquatic ecosystems. Although there were more taxonomic units at the species level than at the functional group level, it remained unclear whether species diversity was more sensitive than functional group diversity to environmental variables. In this study, taxonomic composition and alpha-beta diversity of phytoplankton were investigated in 23 subtropical reservoirs located in the Han River Basin in South China during wet and dry seasons. Structural Equation Modelling (SEM) and Generalized Dissimilarity Modelling (GDM) were employed to validate the response of phytoplankton species and functional group alpha-beta diversities to environmental variables. The results indicated that the community compositions of phytoplankton in eutrophic reservoirs were similar between wet and dry seasons, while there were distinct differences for community composition in oligotrophic-mesotrophic reservoirs between the two seasons. Across all reservoirs, there were no significant differences in alpha and beta diversities of species and functional groups between wet and dry seasons. The SEM and GDM results revealed that total phosphorus was the primary driving factor influencing alpha and beta diversities of species and functional groups in the 23 reservoirs. Meanwhile, the non-linear results of species beta diversity were stronger than the non-linear results of functional group beta diversity, indicating that phytoplankton species exhibited a higher explanatory power in responding to environmental changes compared to that of functional groups. Compared to that of species beta diversity, the response of functional group beta diversity to environmental variables was significantly lower in the dry season. These research findings lead to re-evaluating the common practice relating to the use of phytoplankton functional groups to assess environmental conditions, which may overlook the explanatory power of subtle changes at the species level, especially during periods of habitat diversification in the dry season.