Configuration difference management is the essential action to evaluatewhether the design configuration satisfy the requirement of the experiment/test flight and the representativeness of airworthiness in the process of airworthiness verification experiment/test flight during research of civil aircraft. This paper analysis different kinds of configuration difference before and after airworthiness verification activity from the aspect of single design configuration requirement, the requirement of airworthiness verification experiment/test flight, type certification configuration, single design configuration and manufacture state and put forward the configuration difference management model.