Abstract: The inhibition effect of plant endophyte Bacillus subtilis strain Em7, isolated from wheat roots, against Botrytis cinerea Pers. was studied, by using the antifungal test on medium plates, inhibition test of conidia germination, in vitro inoculation on fruit, and observation with electron microscopy. Confronting incubation of B. subtilis Em7 and B. cinerea on PDA medium resulted in obvious inhibition zones, with the diameter of 2.81 cm. Em7 treatment led to 88.65% failure germination of the B. cinerea conidia. In vitro inoculation assay verified that Em7 treated B. cinerea exhibiting reduced pathogenicity on grape fruit with a lower disease index, and the relative control effect reached 78.92% compared to the controls. Moreover, scanning electron microscopy observation revealed a malformed morphology of the Em7 treated fungus mycelium, with an uneven surface, a local swelling node or constriction, more branches, increased vacuoles, thicken cell wall, and altered cell membrane permeability. The plant endophytic B. subtilis Em7 can effectively inhibit B. cinerea and reduce the fungus pathogenicity.