The forward cabin of some space aircraft is a combination structure of the end socket and the cabin body. After trial assembly without protective layer, it is decomposed and assembled again by bonding the protective layer respectively. During assembly, it is necessary to ensure that the step value of the docking surface meets the requirements. In view of the problem that the end socket has bonded protective layer the and the cabin body has not bonded protective layer, the step value of the docking surface cannot be guaranteed in the assembly, the end socket coordinate axis was established according to the end socket structure and the scan accurate measurement data, the difference value conversion method of measurement data and the qualified method of step value judgment were designed. Measured step value after the replacement end socket was assembled in the cabin body,and the theoretical step value of the original end socket was calculated. Furthermore, the qualification index can be judged and the grinding measures can be made, solving the problem of how to guarantee the step value in the assembly end socket of the unconventional process. Through the end socket assembly test, the effectiveness of the method was verified, which can ensure that the step value of the docking surface meets the requirements. The promotion value of this research in product development stage,batch production stage, and assembly of similar structural products was presented.