The black soldier fly larvae (BSFL) have become a promising candidate for waste disposal and are an ideal feed source for animal nutrition. The uptake of heavy metals could influence the growth of BSFL, but the effects of heavy metal pressures on the gut microbiota of BSFL are largely uncharacterized. Here, we examine the influences of Cu and Cd on the growth and gut microbiota of BSFL as well as the distribution of accumulated heavy metals in the larvae and their feces. Exposure to Cu (from 100 to 800 mg/kg) and Cd (from 10 to 80 mg/kg) did not significantly inhibit the weight gain of BSFL. With elevated exposure doses, the contents of both Cu and Cd accumulated in the bodies and feces of BSFL were remarkably increased. In the BSFL feces, Cu mainly existed as residues, while Cd mainly existed as either water-soluble states (in the low-exposure groups) or residues (in the high-exposure groups). Cd was more readily enriched (47.1%-91.3%) than Cu (<30%) in vivo. More importantly, exposure to Cu and Cd remarkably altered the gut microbiota of BSFL, particularly in the phyla Proteobacteria, Firmicutes and Bacteroidetes. High exposure to the metals (i.e., Cu-800 and Cd-80 groups) substantially decreased the abundances of most of the dominant families, but significantly stimulated the enrichment of Brucellaceae, Enterobacteriaceae, Alcaligenaceae, Campylobacteraceae, and Enterococcaceae. Moreover, the bacterial diversity in the BSFL gut was significantly reduced following high exposure to the metals. These results may fill a gap in our knowledge of the effects of heavy metals on the intestinal microbiome of BSFL.