The invention belongs to the technical field of medicines, and relates to an anti-neoplastic pharmaceutical composition for targeting hedgehog pathway and cell autophagy. The pharmaceutical composition contains a Hedgehog signal pathway inhibitor and a cell autophagy inhibitor. Through pharmacology test proves that the pharmaceutical composition has obvious synergistic effect for treating solid tumors and non-solid tumors, and especially has very obvious antineoplastic effect for drug-resistance chronic myelogenous leukemia. The disclosed pharmaceutical composition has wide antineoplastic activity and good clinic application prospect.