The flavor alterations in bighead carp subjected to varying storage temperatures and the underlying metabolic mechanism were elucidated. Analysis of volatile flavor compounds, electronic nose, free amino acids, ATP-related compounds, and sensory evaluations uncovered a progressive flavor deterioration during storage, especially at 25 °C. Metabolomics-based flavor relating component profiling analysis showed that free fatty acids formed various fatty aldehydes including (E, E)-2,4-heptadienal and nonanal under lipoxygenase catalysis. Alcohol dehydrogenase and alcohol acyltransferases were intimately involved in alcohol and ester generation, while alkaline phosphatase, 5′-nucleotidase, and acid phosphatase were closely associated with IMP, Hx, and HxR conversion, respectively. Aeromonas, Serratia, Lactococcus, Pseudomonas, and Peptostreptococcus notably influenced flavor metabolism and enzyme activities. The metabolism disparities of valine, leucine, isoleucine, lysine, and α-linolenic acid could be the primary factors contributing to flavor metabolism distinctions. This study offers novel insights into the flavor change mechanisms and potential regulation strategies of bighead carp during storage.