Long-term phytoplankton community changes indicate trophic status under nutrient regulations in eutrophic lakes, and the modulated role of climate change scenarios on their indicative function was underestimated. Hence, we analyzed the relative contribution of nutrients and climate factors on the inter-annual and seasonal variations in phytoplankton biomass and composition from 1992 to 2017 in Meiliang Bay, Lake Taihu, China. Five periods of discrete phytoplankton communities were classified according to the inter-annual features. The variations of phytoplankton community composition were observed along the five periods: exclusive cyanobacterial dominance before 2008 shifted to diatom-cyanobacterial codominance in 2008-2010, and cyanobacterial dominance in 2011-2014 shifted to cyanobacterial-diatom codominance in 2015-2017. The phytoplankton biomass pattern typically peaked in the summer, although peaks also occurred in winter 2008-2010 and autumn 2011-2014. Additionally, phytoplankton biomass increased by threefold from 2015-2017, which may have been related to rising air temperature and greater light availability. The variance of phytoplankton community was significantly explained by nutrients (ammonium, nitrate and phosphate) and climatic (air temperature and wind speed) factors. However, the explaining effect of the factors varied among the five periods: nutrients strongly impacted the community composition from 1992-2007, while climatic variables became more important modulators after 2007. These results revealed that climatic factors play importance roles in shaping phytoplankton community and cyanobacterial blooms, the difference of the roles between specific climatic conditions should be considered. Future declines in cyanobacterial blooms require further dual nitrogen and phosphorus reduction and longer recovery times under current climate change scenarios in this and possibly other shallow eutrophic lakes.