The chemical characteristics and volatile compounds profiles in distinct anatomical sites of a farm-raised hybrid catfish (Clarias macrocephalus × Clarias gariepinus) were investigated. Total haem proteins, trimethylamine-nitrogen, TBARS, n-9 oleic acid, n-6 linoleic acid and total concentration of all volatile compounds were all higher in the lateral line with the maximum redness index (p < 0.05). Dorsal muscle lipid contained more eicosapentaenoic acid and docosahexaenoic acid than the other two muscles (p < 0.05). Ventral muscle exhibited the highest fat content (p < 0.05) and was the only muscle discovered to have n-3 linolenic acid. Geosmin and 2-methylisoborneol (2-MIB) were found in all three muscles. Despite the fact that 2-MIB and geosmin are lipophilic compounds, their distribution was unaffected by fat content, with the highest levels in the lateral line (p < 0.05). Odour activity values (OAV) and sensory analyses revealed that not only 2-MIB and geosmin but also (E)-2-nonenal and 1-octen-3-ol, intensified the earthy and muddy odour in catfish muscles. The total off-odour of catfish muscles was influenced by n-9 oleic acid and n-6 linoleic acid, according to the correlation analysis. The off-odour compounds had a substantial negative connection with total n-3 PUFA, as well as the irrelevance with fat content, according to this study.