Transgenic rice expressing Bacillus thuringiensis (Bt) Cry1Ac and Cry2Aa toxins have proven resistant to lepidopteran pests in China, including the striped stem borer, Chilo suppressalis. Identifying the molecular mechanisms through which Cry toxins affect insect pests is essential, both for understanding the nature of their toxicity, and for assessing the potential for the development of resistance to such toxins. In this study, both one-dimensional gel electrophoresis (1-DE), combined ligand blots and mass spectrometry, were used to identify proteins binding to the Cry1Ac and Cry2Aa toxins in brush border membrane vesicles (BBMVs) of the C. suppressalis larvae midgut. Aminopeptidase-N (APN), alkaline phosphatase (ALP), cadherin-like (CAD), ATP-binding cassette transporter subfamily C1 protein (ABCC1), actin, ATPase, alpha amylase, and heat shock protein cognate (HSPC), were detected in Cry1Ac binding bands, and APN, actin, ATPase and HSPC were identified as Cry2Aa potential binding proteins. The novel potential binding protein, delta-aminolevulinic acid dehydratase, was also detected in both Cry1Ac and Cry2Aa binding bands. This is the first study to comprehensively identify the proteins that bind to Cry1Ac and Cry2Aa toxins in C. suppressalis.