Phytoplankton is capable of responding to aquatic conditions and can therefore be used to monitor freshwater reservoir water quality. Numerous classification techniques, including morpho-functional approaches, have been developed. This study examined changes in phytoplankton assemblages and water quality, which were sampled quarterly from July 2018 to April 2019. The purpose was to contrast the applicability of three classification approaches (functional, morpho-functional and morphological-based functional groupings) for understanding the spatial and seasonal distribution of the biomass variance in phytoplankton functional groups and their driving environmental factors in the ecological zones of the Shanxi Reservoir through multivariate analysis. The results showed that the phytoplankton biomass was highest in the watercourse zone and lowest in the transition zone. Furthermore, the Shanxi Reservoir was characterized by several cyanobacteria (Microcystis spp.) and numerous bacillariophytes (Asterionella sp., Navicula spp. and Aulacoseira granulata). After evaluating the advantages and disadvantages of morpho-functional classifications, we determined that water temperature appeared to be an essential factor, and the morphology-based functional group approach provided the best results for demonstrating phytoplankton succession, despite having lower sensitivity than the others. Nevertheless, these approaches are all appropriate for identifying and monitoring phytoplankton community structure in aquatic systems of reservoirs with complex terrains.