Cry1A-type toxins are insecticidal proteins from Bacillus thuringiensis that are widely used to control Lepidoptera pests, and they are believed to be useless for the control of Hemiptera pests. In this paper, the purified Cry1Ab1 toxic core rarely killed peach aphids (Myzus persicae), as its Lethal Concentration 50 (LC50) was up to 1308.6 μg/ml, as measured using the membrane-encapsulation method. We then identified the proteins that bind to the Cry1Ab1 toxic core in M. persicae using pull-down assays and liquid chromatography−tandem mass spectrometry (LC-MS/MS), and then analyzed the associated functions of these proteins using the STRING database. GPN-loop GTPase 2, beta-actin, ATP synthase subunit alpha and an unknown and annotated protein, which are mainly involved in cell phagocytosis, RNA polymerase, cellular oxidative phosphorylation and other related functions, were the proteins that bound to the Cry1Ab1 toxic core. Indications from docking showed that Cry1Ab1 toxic core, ATP synthase subunit alpha and beta-actin or Cry1Ab1 toxic core, ATP synthase subunit alpha and GPN-loop GTPase 2 being a complex to exert effects. Based on the identification of Cry1Ab1-binding proteins from M.persicae, we presented here the molecular clues that Cry1A exert a negative effect on aphid growth and development, and we also proposed that Cry protein had the ability to disturb virus transmission by aphid. The two indications will result in new insights for aphid-effective Cry evaluation and improvement.