In the course of the development of civil aircraft and the subsequent delivery and operation process, it is impossible to avoid the configuration differences existing objectively. The configuration differences include the difference between the single ship and type design, the difference between the single status and single design requirements, and the difference between the manufacture state and the design requirements. It is the key problem and difficulty in the aircraft development process to record the differences exactly, evaluate the effect of differences,and provide effective evidence in order to make clear the limit relevant countermeasure. Based on the fight test aircraft, this paper analyzed the configuration differences of design and the configuration differences of manufacture.Improvement suggestions for management of the configuration differences were proposed.