Host-probiotics of many fish species have not been applied due to the difficulty in isolation and functional verification, and some exogenous probiotics were confirmed to promote the growth performance of fish. Therefore, this study aims to screen the exogenous probiotics that can be used in the culture of Chinese perch and to explore their mechanism of action. Chinese perch were respectively fed with basal diet (CK) supplemented with Clostridium butyricum CB1 (C), Enterococcus faecalis EF1 (E), Bacillus subtilis BS1 (B), and Lactobacillus plantarum LP1 (L) at 1.0 × 108 CFU/g with equal amount for 8 weeks. After feeding, B group presented significantly higher abundance of Bacillus, Lactobacillus, and Paenibacillus, and L group displayed significantly higher abundance of Lactobacillus than CK group. Above increased probiotics species led to higher intestinal lipase activity in B group, intestinal protease activity in L group, and length of intestinal villi and thickness of intestinal wall in B and L groups through fermentation to reduce pH value and secretion of active substances, thus facilitating the nutrient absorption to improve the weight gain (WG). Additionally, B and L groups respectively exhibited higher abundance level of the infectious diseases-related pathway and lower abundance of Aeromonas, which was responsible for higher expression of pro-inflammatory cytokines (p65-NF-κB, IL-Iβ, TNFα, and PAI) and higher blood immune parameter levels (globulin (GLB), total protein (TP), and lysozyme activity (LZM)), eventually improving survival rate. E group significantly inhibited microbial diversity and abundance of Energy metabolism pathway and Amino acid metabolism pathway, which might the reason for the decrease in crude protein content in whole-fish. C groups significantly reduced the microbial diversity and the length of intestinal villi to affect the host's nutrient absorption efficiency, thus causing a decrease in growth performance. Moreover, the imperfection of intestinal villi may allow more LPS to penetrate into the blood, thereby down-regulating the immune status and inducing inflammation, ultimately reducing survival rate. Above results indicated that Bacillus subtilis BS1 and Lactobacillus plantarum LP1 might be used in aquaculture, and probiotics may affect growth performance and gut health by regulating gut microbiota.