To solve the problems of low teaching programming efficiency and poor flexibility in robot welding of complex box girder structures, a method of seam trajectory recognition based on laser scanning displacement sensing was proposed for automated guidance of a welding torch in the skip welding of a spatially intermittent welding seam. Firstly, a laser scanning displacement sensing system for measuring angles adaptively is developed to detect corner features of complex structures. Secondly, a weld trajectory recognition algorithm based on Euclidean distance discrimination is proposed. The algorithm extracts the shape features by constructing the characteristic triangle of the weld trajectory, and then processes the set of shape features by discrete Fourier analysis to solve the feature vector used to describe the shape. Finally, based on the Euclidean distance between the feature vector of the test sample and the class matching library, the class to which the sample belongs is identified to distinguish the weld trajectory. The experimental results show that the classification accuracy rate of four typical spatial discontinuous welds in complex box girder structure is 100%. The overall processing time for weld trajectory detection and classification does not exceed 65 ms. Based on this method, the field test was completed in the folding special container production line. The results show that the system proposed in this paper can accurately identify discontinuous welds during high-speed metal active gas arc welding (MAG) welding with a welding speed of 1.2 m/min, and guide the welding torch to automatically complete the skip welding, which greatly improves the welding manufacturing efficiency and quality stability in the processing of complex box girder components. This method does not require a time-consuming pre-welding teaching programming and visual inspection system calibration, and provides a new technical approach for highly efficient and flexible welding manufacturing of discontinuous welding seams of complex structures, which is expected to be applied to the welding manufacturing of core components in heavy and large industries such as port cranes, large logistics transportation equipment, and rail transit.