Bacillus laterosporus Bl13 has good antagonistic effect on the pathogen of tomato early blight (TEB) disease. A pot experiment was conducted to investigate the effect and mechanism of B. laterosporus Bl13 against TEB disease by measuring biological traits such as plant height, stem diameter, disease index of TEB, activity of plant defense enzyme in leaves, and microbial diversity and community composition in root area. The results showed that B. laterosporus Bl13 could significantly reduce the disease index of TEB disease incidence, increase the activity of defensive enzymes including polyphenol oxidase (PPO) and peroxidase (POD) in leaves, and reduce the effects of the disease on the aboveground and root growth of tomato. Meanwhile, B. laterosporus Bl13 improved soil microbial community structure in the root zone, by significantly increasing the relative abundance of plant growth-promoting bacteria (Bacillus and Pseudomonas) and decreasing that of Olpidium and Haematonectria. The results showed that B. laterosporus Bl13 could enhance plant resistance against TEB disease through improving the activity of defensive enzymes in tomato leaves and increasing the number of beneficial microbes in the root zone.