Gut microbiota of grass carp plays an important role in host. However, detailed information regarding the changes of microbiota after probiotics administration in relation to the gastrointestinal microbiota is absent. In the present study, dietary administration of putative probiotics Shewanella xiamenensis A-1, Aeromonas veronii A-7, and Bacillus subtilisstrains was conducted in grass carp to investigate if there is a discernible alteration in intestinal microbiota and whether the alteration is associated with previous study about the immunity regulation in grass carp. Bacterial 16S rRNA gene sequence-based comparisons of the bacterial communities in the grass carp intestine were detected after 28 days feeding by five diets, and results demonstrated the changes of microbial community composition at genus level. The abundance of Cetobacterium genus with potential immunity function increased. Potential pathogens and probiotics are important constitutions of the intestinal microbiota. Orally taken probiotics considerably reduced the abundance of the potential pathogenic bacteria (e.g., Pseudomonas and Flavobacterium genus) in the intestine. Meanwhile, putative probiotics used in this study were favorable to the reproduction of potential probiotics in THE intestine of grass carp (e.g., Vibrio, Streptococcus, and Enterococcus genus). Moreover, modulation of intestinal environment by the probiotics could impact the abundance of cellulose-degrading bacteria (e.g., Citrobacter genus). Those results suggested that oral probiotics administration can positively improve the composition of intestinal microbial community in grass carp, and this was associated with regulation of immunity in grass carp. Probiotics-induced alteration of microbiota may potentially lower the risk of disease outbreaks during cultivation stage of grass carp.