Some waviness of aircraft surface in special area will seriously affect the aerodynamic characteristics and flight performance. The waviness of these special area need to be measured accurately in order to analyze the affection and to get reference for manufacturing technology improvement. In this paper, a new analysis method of aircraft surface waviness was proposed, which is based on the 3D measurment technology. In the method, the Max/Exa-scan system was used to get the surface information of an actual aircraft, then the analysis functions of CATIA were used to analyze the waviness of measured area. In the end, an example was given to show the feasiblity and effectiveness of this method.