In order to evaluate the effects of dietary Pennisetum sinese Roxb meal on the fat accumulation and intestinal microbiota composition of juvenile grass carp (Ctenopharyngodon idella), three isonitrogenous and isoenergetic purified diets containing 0% (control group), 10% and 20% Pennisetum sinese Roxb meal were designed (protein level 33%, fat level 8%), and fed juveniles grass carp[(28.51±0.04) g] for 8 weeks. Each diet was randomly assigned into triplicate tanks. The results showed that fish fed 10% and 20% pennisetum sinese Roxb meal significantly reduced their abdominal fat index. The microstructure of the tissue section showed the hepatic lipid droplets number and the adipocyte size in the Pennisetum sinese Roxb meal group were reduced compared with the control group. Serum levels of triglycerides (TG), total cholesterol (TC) and non-esterified fatty acids (NEFA) showed a downward trend with the Pennisetum sinese Roxb meal content increasing, and the 20% group had significantly lower values than the control group. The hepatic content of TG, TC, and NEFA were significantly decreased in the Pennisetum sinese Roxb meal supplemented groups. Five lipogenic genes including peroxisome proliferator-activated receptor γ (pparγ) in the liver and abdominal adipose tissue were significantly down-regulated after the fish consuming Pennisetum sinese Roxb meal. Peroxisome proliferator-activated receptor-α (pparα) and other three lipid catabolic genes were significantly up-regulated after the fish fed on the Pennisetum sinese Roxb meal-supplemented diets. The expression of farnesoid X receptor (fxr) gene in the liver was significantly up-regulated in fish feeding Pennisetum sinese Roxb meal. The metagenomics results of the intestinal flora showed the Ace, chao1, Shannon, and Simpson indexes of the intestinal microbiota of grass carp in the 10% and 20% Pennisetum sinese Roxb meal groups were significantly different from those in the control group, indicating dietary Pennisetum sinese Roxb meal increased the abundance and diversity of the intestinal flora of grass carp. From the perspective of phylum classification, the proportion of Firmicutes was significantly lowered in the Pennisetum sinese Roxb meal groups, whereas the proportion of Bacteroides showed an upward trend, and these two bacteria are reported to be associated with fat accumulation in mammals. The results demonstrate that Pennisetum sinese Roxb meal could reduce body fat accumulation, possibly via the improvement of intestinal flora composition in juvenile grass carp.