The quality changes in tilapia belly muscle (BM), dorsal muscle (DM) and tail muscle (TM) were studied and the hypothesis of browning of the fillets was revealed during partial freezing. Compared with DM and TM groups, BM samples had higher thiobarbituric acid reactive substances (TBARS) (0.41 mg malondialdehyde eq/kg at 49 d) and K values (61.81% at 42 d) (P < 0.05). The microstructure of the BM group deteriorated most obviously during storage. Therefore, the BM group was considered to be the fastest to oxidize and deteriorate. In addition, 54 different micromolecular metabolites were identified from tilapia fillets by UHPLC-Q-TOF-MS analysis, and there were significant differences in the micromolecular metabolites in the three parts of tilapia. Therefore, proteins and lipids were degraded by the action of enzymes and microorganisms to produce some amines and small molecular acids, leading to the deterioration of the quality of tilapia fillets.