Abstract: Chinese mitten crab (Eriocheir sinensis) is one of the most popular seafoods in Asian areas. However, the shading from the flexible photovoltaic (FPV) arrays can often affect the pond's environmental conditions and its nutritional quality. This study aimed to evaluate the ecological compatibility of the FPV systems with the pond aquaculture. A systematic analysis was also implemented to clarify their impacts on the pond's physical environment, submerged aquatic vegetation, and cultured organisms. Two treatments were conducted, including the ponds equipped with FPV arrays, and the ponds without photovoltaic facilities as a control (CK). The key environmental factors were determined to be induced by FPV shading, including the light intensity, water temperature, and major water quality. The physiological properties of the dominant submerged macrophyte Elodea nuttallii, the biological performance, and nutritional composition of the Chinese mitten crab tissues were quantitatively evaluated in the culture period. The pond experiment showed that the FPV significantly reduced the underwater light intensity and water temperature (P<0.05), compared with the CK, thereby altering the thermal and light regimes of the pond ecosystem. The light and temperature were combined to regulate the FPV shading. The pond water quality (P<0.05) was significantly improved for the more stable aquatic environment. In the upper water layer, the dissolved oxygen concentration increased by 0.7 mg/L in September. While the ammonia nitrogen concentrations decreased by approximately 0.1 mg/L during August and September, the cyanobacterial biomass was significantly suppressed under FPV shading, with the relative inhibition rates of 18.0% in July and 50.4% in September. In the bottom water layer, the ammonia nitrogen concentrations were consistently reduced by about 0.1 mg/L from July to September. The cyanobacterial biomass exhibited stronger suppression, with the relative inhibition rates of 43.0%, 56.7%, and 60.9% from July to September, respectively (P<0.05). As such, the FPV shading effectively alleviated the eutrophication risks, particularly in deeper water layers. The FPV shading also altered the physiological status of Elodea nuttallii, where the accumulation of the reactive oxygen species was reduced to maintain the basal antioxidant enzyme activities. The stress resistance and physiological stability were enhanced under shaded conditions. At the same time, the ecological function of the submerged macrophytes was also supported in pond systems. In terms of the aquaculture performance, no significant differences were observed between FPV and CK treatments in the hepatopancreas index, gonadosomatic index, condition factor, meat yield, or total edible yield for either male or female crabs (P>0.05). There was no negative effect of the FPV installation on the crab growth, reproductive development, or production efficiency. In nutritional quality, the FPV shading induced moderate but sex-specific changes in certain tissues: The ash content in male gonads decreased by 11.5%, the crude protein content in female gonads increased by 3.0%, and the 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 the muscle nutritional composition between treatments (P>0.05). The FPV shading triggered the adaptive nutritional regulation in the Chinese mitten crabs, with the responses between sexes and tissues, without compromising overall flesh quality or edible value. Overall, the FPV arrays effectively improved the pond environmental conditions and ecological stability compatible with the Chinese mitten crab pond culture. The finding can also provide important scientific evidence for the ecological application and optimization of the fish-light complementation in freshwater aquaculture.