A feeding trial was conducted to investigate the effects of dietary fructooligosaccharide (FOS) on growth performance, body composition, intestinal enzymes activities and histology of fingerling Megalobrama amblycephala. A total of 1200 fish (1.42 ± 0.01 g) were fed diets containing graded levels of FOS (0, 0.5, 1, 2, 4 and 8 g kg−1 diet) for 8 weeks in a recirculating system indoor. The weight gain, specific growth rate (SGR) and survival rate were all improved in dietary supplementation of FOS fed fish. Increasing FOS levels resulted in both higher whole-body lipid and lower moisture contents, whereas ash and protein contents showed no significant differences among all the treatments. Intestinal amylase, protease, Na+, K+-ATPase, alkaline phosphatase, γ-glutamyl transpeptidase and creatine kinase activities all increased with dietary FOS levels up to 4 g kg−1 (P < 0.05). Transmission electron microscopy analysis indicated that microvilli length in the mid-intestine was significantly increased with increased dietary FOS levels (P < 0.05). In conclusion, dietary supplementation of FOS could confer benefits on growth performance, intestinal digestive and absorptive ability, histology of fingerling Megalobrama amblycephala.