Jujube (Ziziphus jujuba), as an edible-medicinal fruit, is an important Chinese herbal medicine, which has several beneficial effects on host such as immunomodulation, antioxidant, and gastrointestinal protection. In the study, the beneficial effects of dietary jujube extract supplementation on digestion, nonspecific immunity and intestinal microbial diversity of rainbow trout (Oncorhynchus mykiss) were investigated. The fish were fed for 56 days with diets containing 0 (control), 0.25%, 0.50% and 1.00% jujube extract, and then gastrointestinal digestive enzyme activities, nonspecific immune genes expressions and intestinal microbial diversity were measured. Intestinal protease and α-amylase activities in 0.25% and 0.50% groups, and lactase activity in 0.50% group were significantly improved. The expression of Cu/Zn-superoxide dismutase (SOD) gene was significantly increased in 0.50% and 1.00% groups. Catalase (CAT) and glutathione S-transferase A (GSTA) were significantly increased in 0.50% and 0.25% groups, respectively, while glutathione peroxidase 1 (GPX1) in 0.50% group, complement 3 (C3) in 1.00% group and transforming growth factor-β (TGF-β) in jujube extract groups were all significantly down-regulated. In the gut microflora, there were significant differences in the gut abundances of three phyla (Bacteroidetes, Tenerictes, and Actinobacteria) and eight genera (Dinghuibacter, Lachnospiraceae_ NK4A136_group, Aeromonas, Pseudarthrobacter, Acetatifactor, uncultured_ bacterium mycobacteriumand Rikenellaceae_RC9) among the four experiment groups. Moreover, the abundances of Aeromonas in 0.25% and 0.50% groups were significantly decreased compared with the control group, while Acetatifactor in 0.25% group and Dinghuibacter in 1.00% group were significantly increased. The clusters of orthologous groups of proteins (COG) functional prediction analysis indicated that these differences of intestinal microflora were mainly in metabolism, cellular processes and signaling, and information storage and processing. These results showed that jujube extract can improve the digestive and immune ability, and induce a positive effect on the intestinal flora of rainbow trout.