Bombyx batryticatus is the dried dead larva of silkworms after infection by a fatal fungi Beauveria bassiana. It’s a challenging task to monitor intrinsic biological macromolecules in this natural medicine. In this study, a novel strategy based on comparative proteomic analysis was developed to disclose inherent differences between processed and highly processed Bombyx batryticatus. First, protein and amino acid contents were determined, and the changes in proteins after highly processing the medicine were profiled through electrophoresis-based technologies. Then, the peptides that originated from the differentiated proteins were eluted under reversed-phase NanoLC and sequenced by orbitrap MSD. It was found that both contents had been significantly decreased after processed Bombyx batryticatus was stir-baked with wheat bran. Additionally, protein bands and spots visualized in SDS-PAGE and 2-DE profiles of the processed product were much brighter than those of the highly processed product, allowing them to be distinguished by electrophoresis profiling readily. Moreover, thirty-two signature proteins were identified as potential biomarkers by NanoLC-orbitrap MSD after in-gel tryptic digestion of specific bands and spots. This work provides a solid scientific basis for quality assessment and control of commercial products of this natural medicine, and the developed novel strategy could ensure its safety and efficacy.