<p>As a new kind of green and environmentally friendly fertilizer, plant growth promotion and disease resistance function microbial fertilizer has become a new trend of agricultural production. In this study, <i>Bacillus velezensis</i> YU18 with high protease yield was isolated from mangrove rhizosphere soil and its genome was analyzed. The fermentation process was optimized and applied to the development of functional microbial fertilizer. The optimal growth temperature of strain YU18 was 30℃, the optimal growth pH was 7, and the strain could adapt to 100&#xa0;g/L high concentration salt environment. The optimum process of protease production was sucrose as fermentation carbon source, soybean meal or peanut bran as fermentation nitrogen source, Na⁺ or K⁺ as inorganic salt ion, fermentation temperature was 37℃, fermentation pH was 7. Inorganic nitrogen as fermentation nitrogen source hardly produces protease. There were abundant NRPS and PKS gene clusters in the genome of strain YU18, most of which were not similar to the known gene clusters, and there were resistance genes to Cu, As, Cr, Hg and Cd. In particular, it can tolerate Cu concentrations below 500&#xa0;mg/L. The functional microbial fertilizer prepared by the fermentation of strain YU18 contains IAA and siderophores that promote plant growth, and has broad-spectrum antagonistic function against plant pathogens. These findings provide a basis for further promotion and development of the application of <i>Bacillus velezensis</i>.</p>