The global environment has experienced rapid changes over the past four decades, including global climate warming, radiation dimming and brightening, wind stilling, and abnormal climate fluctuations. Meanwhile, strong human activities such as dam construction, bank hardening and water diversion and drainage have happened in Lake Taihu catchment. All these changes of natural environments and human activities have profoundly reshaped the physical environments and processes of Lake Taihu, which have further strongly driven the evolution of lake ecosystem structure and function. Based on historical literatures and documents, as well as long-term observations of meteorology, hydrology and Secchi disc depth (SDD), this study aims to systematically explore the spatial distribution and long-term change characteristics of physical environment in Lake Taihu, such as air temperature, water temperature, water level, wind speed and SDD. Meanwhile, we will elucidate the synergistic effects of air temperature and wind speed, water level and SDD and their potential ecological environmental significances for algal bloom outbreaks and aquatic macrophytes loss. Due to the global changes and rapid urbanization, the air temperature and water temperature of Lake Taihu have been increasing continuously in the past 40 years, while the wind speed near the ground has been decreasing continuously. Lake warming and decreasing wind speed facilitate the growth of algae and the floating accumulation of cyanobacteria bloom, which to some extent increases the observation frequency and area of cyanobacteria bloom. In order to control the flood and meet the increasing demand of water resources in the basin, the water level of Lake Taihu is increasing slowly due to dam control and water diversion. However, the increase of pollutants entering the lake and the development of eutrophication gradually decrease SDD. Therefore, the significant decrease of the ratio of SDD to water level (water depth) was observed in Lake Taihu, which significantly decreased the available light intensity at the bottom of the lake, and deteriorate the underwater light environment. All these changes have resulted in the loss of aquatic macrophytes and greatly driven the degradation of macrophyte-dominated ecosystem in Lake Taihu. The long-term changes of lake physical environment have gradually expanded the algae habitat space of Lake Taihu, compressed the macrophyte habitat space, accelerated the shift from a clear macrophyte-dominated state to a turbid algal-dominated state, and enhanced the long-term maintenance of algal-dominated ecosystem. Therefore, our findings highlight the importance of long-term physical environment monitoring data for deeply understanding ecosystem response to global climate change and human activities. The profound changes in physical environment has also partially offset the control of algal biomass and cyanobacteria bloom caused by the reduction of nutrients in the basin and the decrease of nutrients in the lake, which will increase the difficulty of prevention and control of cyanobacteria bloom and lake eutrophication in Lake Taihu. This means that in the future, more strict standards are needed for controlling pollution and nutrients, and the effective control of lake physical environment such as water level is the adaptive management strategy to deal with the aggravation of algal bloom and the restoration of macrophyte-dominated ecosystem.