Abstract: To clarify the mechanisms by which shading from flexible photovoltaic (FPV) arrays affected pond environmental conditions and the nutritional quality of Chinese mitten crab (Eriocheir sinensis), a pond experiment was conducted using two treatments, including ponds equipped with FPV arrays and ponds without photovoltaic facilities as a control (CK). The study aimed to evaluate the ecological compatibility of flexible photovoltaic systems with pond aquaculture by systematically analyzing their impacts on the pond physical environment, submerged aquatic vegetation, and cultured organisms. The effects induced by FPV shading on key environmental factors, including light intensity, water temperature, and major water quality parameters, the physiological characteristics of the dominant submerged macrophyte Elodea nuttallii, and the biological performance and basic nutritional composition of Chinese mitten crab tissues were quantitatively evaluated throughout the culture period. Compared with the CK treatment, FPV significantly reduced underwater light intensity and water temperature (P<0.05), which altered the thermal and light regimes of the pond ecosystem. Through the coupled regulation of light and temperature, FPV shading was associated with an overall improvement in pond water quality (P<0.05) and contributed to a more stable aquatic environment. In the upper water layer, dissolved oxygen concentration increased by 0.7 mg/L in September, while ammonia nitrogen concentrations decreased by approximately 0.1 mg/L during August and September; meanwhile, cyanobacterial biomass was significantly suppressed under FPV shading, with relative inhibition rates of 18.0% in July and 50.4% in September. In the bottom water layer, ammonia nitrogen concentrations were consistently reduced by about 0.1 mg/L from July to September, and cyanobacterial biomass exhibited stronger suppression effects, with relative inhibition rates of 43.0%, 56.7%, and 60.9% from July to September, respectively (P<0.05), indicating that FPV shading effectively alleviated eutrophication risks, particularly in deeper water layers. FPV shading also altered the physiological status of Elodea nuttallii by reducing the accumulation of reactive oxygen species and maintaining basal antioxidant enzyme activities, which enhanced its stress resistance and physiological stability under shaded conditions and supported the ecological function of submerged macrophytes in pond systems. In terms of aquaculture performance, no significant differences were observed between FPV and CK treatments in hepatopancreas index, gonadosomatic index, condition factor, meat yield, or total edible yield for either male or female crabs (P>0.05), indicating that FPV installation did not negatively affect crab growth, reproductive development, or production efficiency. Regarding nutritional quality, FPV shading induced moderate but sex-specific changes in certain tissues: ash content in male gonads decreased by 11.5%, crude protein content in female gonads increased by 3.0%, and crude protein content in the hepatopancreas increased by 15.8% in males but decreased by 15.7% in females, while no significant differences were detected in muscle nutritional composition between treatments (P>0.05). These results suggested that shading by FPV triggered limited adaptive nutritional regulation in Chinese mitten crabs, with distinct responses between sexes and tissues, without compromising overall flesh quality or edible value. Overall, the study demonstrated that flexible photovoltaic arrays effectively improved pond environmental conditions, enhanced ecological stability, and were compatible with Chinese mitten crab pond culture, providing important scientific evidence for the ecological application and management optimization of fish-light complementation systems in freshwater aquaculture.