Flavor and nutritional value are important qualities of freshwater fish products, but the key factors affecting these quality parameters remain unclear. In this study, four typical aquaculture modes, including the commercial feed treatment (control), faba bean treatment (FBT), grass powder treatment (GPT), and waving water treatment with commercial feed (WWT), were used to explore the regulatory effect of water quality and feed (eaten and uneaten) on the flesh flavor and nutrition in grass carp (Ctenopharyngodon idella), a freshwater fish of the largest global production. During the culture period (90 days), water quality parameters of the four modes were measured every 15 days, and the flavor quality was evaluated by volatile flavor compounds detection and electronic nose analyzer. Flesh crude protein, crude fat, free fatty acid and free amino acid profiles were also determined. The results showed that, in the late period, the FBT mode had the poorest water quality with highest concentrations of nitrite and nitrate, while the GPT mode has the best water quality among the four modes. Most flesh flavor compounds found in the flesh of the control, GPT and WWT modes were pleasant. In the FBT mode with the poorest water quality, on the other hand, we found lower flavor quality (higher contribution of fishy compounds), higher water content, and lower contents of crude protein, crude fat, free fatty acids and free amino acids, compared to the other three modes. Correlation analyses showed that nitrite and nitrate are probably key water quality factors affecting the flavor quality and nutritional values besides eaten feed and uneaten feed factors. This study can serve as an important reference for ecological regulation and feeding administration of flesh quality in freshwater aquaculture fish.