Abstract: To investigate effects of dietary rapeseed meal on the growth performance, intestinal morphology, microflora, and the expression of small peptide transport related genes of grass carp (Ctenopharyngodon idellus), four isonitrogenous and isolipidic diets were formulated by adding 0, 5%, 10% and 15% fermented sesame meal to replace 0, 11.8%, 23.5% and 35.1% of rapeseed meal protein respectively, which were named as control group, trial group 1, trial group 2 and trial group 3. The experiment was carried out in an indoor recirculating system with three replicates in each group. Triplicates of 20 fish initial body weight of (99.98±0.69) g were fed to apparent satiation with four experiment diets twice a day for 45 days. The results showed no significant difference in weight gain rate (WGR), specific growth rate (SGR) and protein efficiency rate (PER) among all the groups, and WGR, SGR and PER of trial group 1 and 2 were slightly higher than those of the control group (P>0.05). Feed conversion ratio (FCR) of trial group 1 and 2 was slightly lower than that of the control group (P>0.05). The heights of intestinal villi in the trial groups were significantly higher than those of the control group (P<0.05), while the depth of crypt in the trial groups was significantly lower than that of the control group (P>0.05). The ratio of villi height to crypt depth (V/C) in the trial groups were significantly higher than that of the control group (P<0.05). Dietary fermented sesame meal significantly induced Lactobacillus and Bacillus (P<0.05) and significantly decreased Escherichia coli and Aeromonas (P<0.05). The expressions of CDX2, Sp1 and PepT1 genes increased significantly at first and then decreased with the increasing fermented sesame meal inclusion (P<0.05). These results suggest that the optimum proportion of fermented sesame meal replacement dietary rapeseed meal was 11.8%—23.5%.