Because of the age of relics and the lack of historical data, the geometric forms of missing parts can only be judged by the subjective experience of repair personnel, which leads to varying restoration effects when the geometric structure of the complex relic is reconstructed. Therefore, virtual repair effects cannot fully reflect the historical appearance of cultural relics. In order to solve this problem, this paper presents a virtual restoration method based on the multiscale spatial geometric features of cultural relics in the case of complex construction where the geometric shape of the damaged area is unknown, using the Dazu Thousand-Hand Bodhisattva statue in China as an example. In this study, the global geometric features of the three-dimensional (3D) model are analyzed in space to determine the geometric shape of the damaged parts of cultural relics. The local geometric features are represented by skeleton lines based on regression analysis, and a geometric size prediction model of the defective parts is established, which is used to calculate the geometric dimensions of the missing parts. Finally, 3D surface reconstruction technology is used to quantitate virtual restoration of the defective parts. This method not only provides a new idea for the virtual restoration of artifacts with complex geometric structure, but also may play a vital role in the protection of cultural relics.