Fermentation is a promising method to improve the utilization of soybean meal (SM) by fish, and strain is the core of fermentation process. In this study, the effects of Lactobacillus paracasei fermentation on the SM quality were investigated. Also, an 8-week feeding trial was conducted to compare the performance of SM and L. paracasei fermented SM (LPFSM) in diets for turbot. Juvenile turbots (13.50 ± 0.13 g) were randomly divided into nine treatments fed on diets with 0% (FM, control), 15% (S15/L15), 30% (S30/L30), 45% (S45/L45), and 60% (S60/L60) of fishmeal protein replaced by SM or LPFSM respectively. The results showed that fermentation remarkably increased the lactic acid and decreased the anti-nutritional factors in SM. Furthermore, fishmeal could be replaced by SM up to 30% or by LPFSM up to 45% based on the growth performance. Typical groups (FM, S45, and L45) with significant differences in growth were selected for further analysis. Reduced villus height and widened lamina propria were observed in the S45 group, while no significant pathological symptom was found in the L45 group. The mRNA levels of the apoptosis-related genes (bax, p53, and caspase3) and tight junction-related gene (tricellulin) in the S45 group were significantly up-regulated or down-regulated, respectively, while the L45 group remained similar to the FM group. The mRNA levels of tight junction-related genes (zo-1 and occludin) were significantly down-regulated in both S45 and L45 groups compared to the FM group. Furthermore, dietary LPFSM modified the intestinal microbiota by regulating the dominant bacterial phyla (Proteobacteria, Firmicutes, and Actinobacteria) and genera (Cobetia, Pseudomonas, and Lactobacillus), and making the overall microbiota profile more coherent with FM-fed fish. Collectively, L. paracasei fermentation significantly improved the SM quality, and fishmeal could be replaced by LPFSM up to 45% without adverse effects on growth and intestinal health of turbot.