Concerning the difficulties such as large errors and low efficiency in traditional detection method of the skin seam and the defects based on 2D laser scanning, a method of the skin seam based on 3D laser scanning is proposed and corresponding software is developed. Methods and steps of de-noising, critical points recognition and extraction for the skin seam testing based on 3D point cloud are proposed. Based on the influence of gap and flush on the aerodynamic shape, the actual geometry structures are analyzed. Compared with theoretical structures, the mathematical model of gap and flush is established. The calculate accuracy is verified through experiments of simulation work piece. Field experiments show that the detection method is feasible and compared with two-dimensional laser detection, the accuracy and repeatability are better. The gap measurement accuracy reaches 0.04mm as well as the flush measurement accuracy reaches 0.02mm, which meet the needs of the skin seam detection and provid the numerical basis for the analysis of the influence of gap and flush on the assembly quality.