Due to the influence of external loads such as gravity, the structure of aircraft assembly positioning tool is inevitably deformed, which directly affects the assembly accuracy of aircraft structure. However, due to the occlusion of product shape, the traditional vision-based structural deformation measurement method can’t directly obtain the structural deformation of tooling. In this paper, an accurate and fast prediction method of terminal deformation of positioning structure based on laser data inversion is proposed. The positioning structure is scanned and measured by laser scanner, and the measured numerical model is obtained. Based on the digital simulation model of the positioning structure, the simulation data set is obtained automatically, and the mapping model between the deformation of the terminal and the deformation of the visible region is established by using the multi-layer perceptron network. On this basis, the inverse differential optimization method of the terminal deformation of the tool structure is constructed, and the inverse solution of the terminal deformation of the positioning tool structure is realized. The results show that the maximum error between the predicted value and the measured value is 8.25%, which verifies the validity of the proposed method.