To investigate the adherence of Bacillus subtilis and its inhibitory of Aeromonas hydrophila, the adherence rate of B. subtilis, its inhibition rate of A. hydrophila, and various physiological and biochemical indexes were detected in the intestinal epithelial cells of grass carp. The results showed that after treatment of B. subtilis alone, cell morphology, methyl thiazolyl tetrazolium optical density (MTT OD) value, lactate dehydrogenase (LDH), alkaline phosphatase (AKP) and glutamic oxalacetic transaminase (GOT) activity were unsignificantly changed (P>0.05), but the activities of Na+, K+-ATPase and glutamicpyruvic transaminase (GPT) significantly increased (P<0.05) at 3 h and 6 h, respectively. The cell shape was obviously changed by A. hydrophila from ellipse to irregular shape and the number of dead cells in the culture medium increased. Meanwhile，A. hydrophila could significantly increase MTT OD value and LDH activity in the culture medium, and significantly decrease the activities of Na+,K+-ATPase, GOP and GPT in the cells (P<0.05). The adherence experiment showed that B. subtilis could significantly reduce the adhesion of A. hydrophila to grass carp intestinal cells. In brief, adhesion and damage of A. hydrophila to intestinal epithelial cells were inhibited by B. subtilis.