Using black soldier fly (Hermetia illucens) larvae in treatment of livestock manure is a promising technology. In this study, high-throughput sequencing was used to analyze the microbial community in chicken manure before and after treatment with H. illucens larvae. In fresh chicken manure, the most abundant bacterial phylum was Firmicutes (55.58%) followed by Bacteroidetes (24.52%) and then Proteobacteria (12.29%). After treatment of the manure with H. illucens larvae for 15 days, the abundance of Firmicutes increased to 97.72% while that of Bacteroidetes and Proteobacteria decreased. Concomitantly, the most abundant genera of fungi in chicken manure changed from Kernia (46.19%) and Microascus (17.22%) to Penicillium (46.82%) and Aspergillus (45.22%). Correlation-network analysis showed the existence of strong and complex correlations between the dominant operational taxonomic units (OUT) of bacteria and fungi. While most of these correlations were positive, three specific genera, namely g_norank_f_Bacillaceae, Penicillium, and Aspergillus exhibited negative correlations with the remaining genera. These three genera were highly abundant in the intestines of H. illucens and in chicken manure treated with H. illucens larvae. Based on 16S rDNA microbiome-function predictions, the metabolic pathways associated with sugars, amino acids, and organic pollutants inside the intestinal tract of H. illucens were enriched versus those of the other three groups. In summary, the treatment of chicken manure with H. illucens larvae significantly reduced the microbial diversity, while strongly increasing organic metabolism in the intestinal bacteria. This technology shows the potential for applications in livestock manure treatment.