The management of rural waste, particularly agri-food waste, poses a major challenge to the ecosystem health. This study investigated the efficacy of black soldier fly larvae (Hermetia illucens L., BSFL) bioconversion for agri-food waste under independent treatment or co-treatment strategies using chicken manure and food waste as a model system. The results showed a synergistic effect of co-treating agri-food waste from different sources. The co-treatment strategy enhanced bioconversion efficiency, resulting in a 1.31-fold waste reduction rate and a 1.93-fold bioconversion rate. Additionally, larval growth performance and biomass quality of BSFL were improved, while lauric acid and oleic acid were enriched in the larval fat from the co-treatment strategy. 16S rRNA amplicon sequencing revealed that the co-treatment strategy reshaped both the residue and larval gut microbiota, with distinct enrichment of taxonomical biomarkers. Furthermore, under this strategy, metabolic functions of the residue microbiota were significantly activated, especially carbohydrate, amino acid, and lipid metabolism were enhanced by 16.3%, 23.5%, and 20.2%, respectively. The early colonization of lactic acid bacteria (Weisella and Aerococcus) in the residue, coupled with a symbiotic relationship between Enterococcus in the larval gut and the host, likely promoted organic matter degradation and larval growth performance. Scaling up the findings to a national level in China suggests that the co-treatment strategy can increase waste reduction quantity by 86,329 tonnes annually and produce more larval protein and fat with a market value of approximately US$237 million. Therefore, co-treatment of agri-food waste streams using BSFL presents a sustainable solution for rural waste management that potentially contributes to the achievement of SDG2 (Zero Hunger), SDG3 (Good Health and Well-Being), and SDG12 (Responsible Consumption and Production).