The present study assessed the effects of probiotic bacterium Bacillus coagulans ATCC 7050 (BC) fed at different inclusion levels (0 (BO), 1 × 106 (BC1), 1 × 107 (BC2) and 1 × 108 (BC3) CFU g−1 feed) on growth, feed utilization, body composition, intestinal morphology, microflora, immune response, and resistance to Vibrio parahaemolyticus infection in Litopenaeus vannamei. After 56 days of the feeding trial, the survival rate ranged from 83.33 to 94.17% with no significant difference between dietary treatments (P > 0.05). Dietary probiotic supplementation also affected the intestinal microflora composition. At the phylum level, Proteobacteria accounted for the majority of bacteria followed by Bacteroidetes irrespective of the group. At the genus level, the abundance of opportunistic pathogenic bacteria, such as Vibrio, Tenacibaculum, and Photobacterium significantly decreased (P < 0.05) with an increasing probiotic concentration, and BC3 group experiencing the least. Additionally, increasing probiotic inclusion in diet downregulated the abundance of Muricauda, Kangiella, and Shewanella in shrimps, with the least, observed in the BC3 group. However, beneficial bacteria Pseudoalteromonas significantly increased (P < 0.05) in the intestines of shrimp fed BC3 diet (P < 0.05) compared to other groups including the control. Compared to the control, a significant increase (P < 0.05) of the probiotic treated groups in the final weight, weight gain rate (WGR), specific growth rate (SGR), condition factor (K), activity of lysozyme (LYZ), acid phosphatase (ACP), superoxide dismutase (SOD), total protein (TP), albumin (ALB) in serum, glutathione peroxidase (GSH-Px) in serum and liver, and a significant decrease (P < 0.05) in feed conversion ratio (FCR), triglyceride (TG) in serum, and Malondialdehyde (MDA) in serum and liver were achieved. Increasing probiotic treatment again improved the digestive ability, thus; a significant increase in the activities of lipase, amylase, trypsin, and an enhancement in the villus height, villus width, and muscle thickness of the intestines of the shrimps which correspondingly alleviated intestinal injury. Furthermore, the supplementation of probiotics in challenge test significantly (P < 0.05) enhanced the resistance of shrimp against V. parahaemolyticus infection recording BC3 to receive the highest relative percentage survival (RPS) value of 76%. In conclusion, higher inclusion levels of probiotic BC at 1 × 108 CFU g−1 feed (BC3) in diets can be considered to enhance the growth, intestinal morphology and microflora, immune response and resistance to Vibrio parahaemolyticus of L. vannamei.