Citrus fruit is susceptible to Penicillium mold infection. Biocontrol with utilization of antagonistic microorganisms against postharvest diseases is regarded as an effective and eco-friendly approach in citrus fruit storage. Here, the complete genome of biocontrol strain w176 was obtained with a full length of 3,929,790 bp, and it consists of 12 potential gene clusters which might be responsible for antagonistic metabolites biosynthesis, strain w176 was identified as Bacillus velezensis by genome alignments eventually. Meanwhile, strong restrictions of spore germination rate (SGR) and hyphae elongation were detected when strain w176 was co-incubated with P. italicum, the inhibitory of SGR at 6 h, 9 h and 12 h was 10.00%, 49.59% and 23.53%, respectively. And the inhibitory of hyphae elongation was 35.56% at 12 h. It was also found that strain w176 exhibited notable growth space competition in the co-incubation. Moreover, significantly enhanced activities of catalase and chitinase in citrus fruit were presented 2 d and 3 d post-inoculation with strain w176. Further, citrus fruit treated by strain w176 PDB culture (PBC) or its culture filtrate (CFS) displayed significantly reduced virulence of P. italicum contamination, the decreased disease symptoms of CFS and PBC were 30.32% and 85.22%, individually. The inhibitory disease rate of PBC was 25%. This study reveals that strain w176 has high potential to be applied as bio-pesticide in citrus preservation. The data attained in this research might be helpful for citrus blue mold control, and could provide basis for the bio-preservation study in postharvest fruit.