A 63-day feeding trial was conducted in northern snakehead to observe the effects of a dietary soybean meal substitution on the microbiota community, morphology and inflammatory cytokine gene expression in the intestine. Four isonitrogenous and isoenergetic diets containing increasing levels of soybean meal were used to replace 0%, 25%, 50% and 75% of the defatted fishmeal (diets are referred to G1, G2, G3 and G4, respectively). Different dietary soybean meal substitutions significantly affected the intestinal microbiota composition. At the phylum level, Firmicutes abundance was the lowest in the G4 group, in contrast with Proteobacteria, Bacteroidetes and Planctomycetes. At the genus level, significantly lower abundance of Lactococcus, Geobacillus, Pseudomonas, Streptococcus, Bacillus and Acinetobacter,but higher abundance of Cetobacterium, Planctomyces, Shewanella, Thermomonas, Rubrivivax and Carnobacterium was observed in fish fed the G4 diet. With increased dietary soybean meal, the thickness of the muscularis, the height of the fold and the height of the microvillus in the distal intestine decreased, but the relative expression of IL-1β, IL-10 and IL-17F was significantly up-regulated. In conclusion, more emphasis should be placed on the functionality of intestinal microbiota and the pathogenesis of mucosal inflammation to assess the effects of diet and fish intestinal health through intestinal microbiota profiling.