A pressing problem facing to missile designer is to identify the cross section loads of missile load by measured strains data which would be conveniently obtained in the flight test. A load identification method based on the measured strain data of the surface of the missile body is introduced to determine the equivalent bending moment and the axial force of the cross section. In order to eliminate the interference of the fault points of the measured data, a defect rejection principle based on linear correlation theory is presented to improve the reliability of the identification method. A verification test is designed to verify the accuracy and reliability of the identification method. Results show that the method has the high identification accuracy and can be applied to the engineering practice.