Abstract: In order to promote the resource utilization of organic waste by insects and reduce the risk of pathogenic microorganism transmission, the killing efficiency of pathogenic microorganisms in the process of transforming chicken manure by black soldier fly larvae combined with Bacillus velezensis was studied. By using Staphylococcus aureus as the indicator bacteria, the change trend of pathogenic bacteria in chicken manure was discussed by detecting the change of the number of Staphylococcus aureus during the transformation process. Then, the microbiome technology was further used to analyze the microorganism changes in chicken manure and predict the changes in the abundance of pathogenic microorganisms. The results showed that the number of bacteria in the treatment group of chicken manure transformed independently by black soldier fly larvae (CK group) was slightly increased and then gradually decreased, while the number of bacteria in the treatment group of chicken manure transformed by black soldier fly larvae combined with Bacillus velezensis (T group) was rapidly decreased. By the 192nd hour, the number of bacteria in the chicken manure of T group was 0.2×10⁸ CFU·g⁻¹, which was significantly lower than that in the chicken manure of CK group (1.0×10⁸ CFU·g⁻¹). The number of Staphylococcus aureus in the chicken manure of T group and CK group decreased rapidly, and decreased to 7.9×10³ CFU·g⁻¹ and 8.7×10² CFU·g⁻¹ by the 192nd hour, respectively. The number of Staphylococcus aureus in T group was significantly lower than that in CK group, indicating that Bacillus velezensis assisted the transformation of chicken manure by black soldier fly larvae could significantly reduce the number of Staphylococcus aureus in the chicken manure. The addition of Bacillus velezensis increased the microbial diversity in the chicken manure transformed by black soldier fly larvae, had a significant effect on the microbial composition in the chicken manure at the early stage of transformation, and inhibited the reproduction of Pseudogracilibacillus and Ignatzschineria species. However, it had no obvious effect on the microbial composition in the later stage. The results of bacterial function analysis showed that the potential pathogenic microorganisms in T group were significantly lower than those in CK group at 72 h, indicating that Bacillus velezensis had strong inhibitory activity against the potential pathogenic microorganisms. The results of this study provided a reference for the biosafety to apply black soldier fly larvae and functional microorganisms to produce the high-value alternative proteins from organic waste.