Through a systematic review of 94 pieces of literature related to the impact of floating photovoltaic power stations on aquatic ecological environments, the effects of such power stations on abiotic factors in water bodies (water temperature, dissolved oxygen concentration, nutrient concentration, and pollutant distribution) and aquatic organisms (phytoplankton, aquatic plants, zooplankton, fishes, and birds) were analyzed. It concludes that the photovoltaic panel coverage ratio is the core factor driving ecological effects. Floating photovoltaic power stations reshape phytoplankton community structures through light-thermal coupled stress, inhibit the photosynthesis of submerged plants, alter fish metabolic rhythms and birds’ migration behaviors, and trigger cross-trophic-level ecological cascade effects. By combining zonal layout and material optimization while balancing power generation benefits and ecological protection, a dynamic regulatory strategy for the floating photovoltaic coverage ratio is used: Coverage ratio in core water areas should be less than 30%, while that in ecological buffer zones should be set between 30% and 60%. It also points out the need for future research to further analyze the superimposed response mechanisms of photothermal effects and climate change, construct hydrodynamic-ecological coupling models, and promote the development of floating photovoltaic power generation toward a sustainable model featuring multi-energy complementarity and ecological synergy.