For high-value aircraft, in order to ensure their stealth, pneumatic and safety characteristics, surface geometric defects such as unacceptable rivet height and seam width must be accurately detected during the manufacturing process. These defects need to be controlled within a very small scope of error. Traditional defect detection methods are difficult to meet the actual requirements of manufacturing of advanced aircrafts in terms of information dimension, detection accuracy and efficiency. In this paper, a new method of high-precision 3D defect detection for controlling riveting and seam quality is proposed. For the complexity of illumination distribution on aircraft surface, first, an accurate surface measurement method based on fringe projection is proposed. Then, based on two-dimensional and three-dimensional information, a method of automatic identification and location of rivets and seams is developed. Finally, a visualization method based on augmented reality is proposed to help improve the operator's work efficiency. The experimental results show that the method has high detection accuracy and practicability.