Multiple organic wastes can be fully utilized in modern aquaculture and agriculture, such as crop straw, animal manure, and kitchen waste. Particularly, the severe shortage of feed raw material resources has been the bottleneck to restricting sustainable development in China in recent years. Fortunately, the bioconversion of organic wastes can be an effective way to alleviate the shortage of feed protein resources and the pressure on the ecological environment. Among them, the saprophytic chain insects can be used to promote the comprehensive utilization rate, due to the special ecological functions and the strengthening effect of beneficial microorganisms. The organic matter in the waste can be decomposed and then converted into high-quality proteins and fertilizers. However, the relatively low market acceptance of maggots as feed has been constrained by the uneven physicochemical properties of products. Therefore, it is of great significance to promote the development of the insect industry. This study aims to reveal the physicochemical properties and underlying mechanisms of products during the bioconversion of organic wastes using saprophytic chain insects. The physicochemical properties of maggots and insect feces in the bioconversion of the pretreated kitchen wastes -saprophytic chain were also investigated using a fat analyzer, amino acid analyzer, optical microscope, UV-Vis spectrophotometer, atomic fluorescence spectrometer, atomic absorption spectrometer, high preparative liquid chromatograph, and liquid chromatography/tandem mass spectrometry. High-quality protein resources and fertilizers were obtained during this time. Furthermore, the effect of kitchen waste bioconversion using fly maggots on the product properties was explored to determine the hazardous substances free. The results show that the fly maggots presented the best overall performance when fed for four days. Meanwhile, the protein and fat contents of maggots exceeded 14.79%, and 6.80%, respectively. The amino acid composition of maggots basically corresponded to the recommended value of FAO/WHO. The content of harmful microorganisms and mold in maggots was less than the maximum allowable amount of microbial feed additives, which could be used as a substitute for the third-grade red fish meal of feedstuff in China. The enrichment effect was achieved in the heavy metal elements. The bioaccumulation coefficients of maggots for the heavy metal elements, such as As, Pb, Hg, Cd, and Cr were 0.08, <0.01, 0.17, 3.71, and 0.04, respectively. Maggots shared the strongest bioaccumulation of Cd, followed by Hg, while the enrichment of Pb was relatively weak. The content of heavy metal elements in the insect feces was significantly reduced after bioconversion treatment, which were 0.25, 1.50, 0.03, <0.01, and 10.90 mg/kg, respectively. At the same time, the content of organic matter in the insect feces was 44.34%, which was 11.71% lower than that of kitchen wastes, indicating the reasonable content of N, P, and K. A high-quality fertilizer can be expected when the content of organic matter was not significantly different from other samples. The finding can also provide the theoretical foundation and basic data to support the efficient utilization of multiple organic wastes and the high-value transformation of agricultural wastes.