[Objective] This work aimed to uncover the inhibitory effects of Bacillus velezensis L-1 on pear gray and blue mold, the inhibitory stability of its cell-free supernatant, and understand the molecular mechanism underlying the biocontrol processes.[Methods] We analyzed the inhibitory effects of strain L-1 on pear gray and blue mold both in vitro and in vivo, and observed the influences of strain L-1 on the mycelium growth of pathogens by microscopes. We determined the inhibitory stability of strain L-1 on Botrytis cinerea by oxford cup method and performed the complete genome sequencing of strain L-1 by Pacbio RSⅡ platform. We also annotated the obtained sequences through different protein databases to predict the mechanisms involved in the biocontrol processes.[Results] The control efficacy of strain L-1 against pear gray and blue mold was 92.88% and 77.47% respectively, and strain L-1 caused the swallow and abnormal growth of the pathogens' mycelium. Strain L-1 could grow normally in the broth containing 10% (W/V) NaCl, and its cell-free supernatant showed stable inhibitory effects against pear gray mold under acid, alkali, UV light, heat and protease treatments. Complete genome sequence analysis showed that there were 112 genes involved in the metabolism of different carbons, indicating its ability to grow on different carbon sources. Strain L-1 contained genes encoding the alimine and trehalose, that are related to stress resistance. Strain L-1 contained gene clusters related to the biosynthesis of a variety of polypeptide and polyketide compounds, such as surfactin, fengycin, bacillibactin, bacillaene, macolactin, difficidin, and bacilysin, and the genes encoding enzymes like β-1,3-glucase and chitinase, that could hydrolyze the pathogen cell wall. In addition, strain L-1 contained genes related to the biosynthesis of actoin, which could induce host resistance.[Conclusion] B. velezensis L-1 has the potential as an effective biocontrol agent.