Hemibarbus maculatus is a common economic fish in the midstream and downstream of the Jialing River. In order to resolve the difficulties in aquacultural cultivation, we tested the intestinal and liver digestive function of wild and cultured Hemibarbus maculatus. Histological methods and special biochemical staining methods were used to compare the differences of morphological structure, goblet cells, argyrophil cells, lymphocytes and Na+/K+ATPase in the intestine, and the morphological structure, glycogen and lipid in the liver between the two kinds of Hemibarbus maculatus. The results showed that higher amount of fat was found to attached to the gut, lower Na+/K+ATPase vitality in the foregut and hidgut (p < 0.01) and lower number of goblet cells in the hindgut (p < 0.01) of the cultured Hemibarbus maculatus when compared to the wild ones. The number of the argyrophilic cells did not show significant differences between the two kinds, but the number of lymphocytes was significantly lower in the segments of gut in cultured. This suggests the absorptive function and intestinal immunity are weaker in the cultured Hemibarbus maculatus. In addition, more glycogen and lipid were found in the liver of cultured fishes, which indicates the decreased digestive function of the cultured Hemibarbus maculatus. In conclusion, the intestinal digestion, absorption and lymphocytes level of the wild are generally better than those of the cultured, and more hepatic lipopexia and glycogen are present in the cultured ones. Future aquacultural activities should consider these changes when facing pragmatic problems.