Abstract Assembly plays a crucial role in industrial manufacturing in industrial manufacturing, but the efficiency of conventional manual methods for parts pairing is limited. Previous research has demonstrated the feasibility of deep learning for point cloud feature extraction and 3D reconstruction. An innovative method utilizing deep learning for high-precision feature extraction and surface reconstruction is introduced to optimize parts pairing in this paper. Geometric dimensions and surface topography data are obtained by defining key assembly features and utilizing the Random Sample Consensus method. Deep learning is then used to directly regress the Surface Distance Function from point samples, facilitating comprehensive part surface modeling and supporting assembly simulation in the digital twin. To validate this approach, a case study demonstrates successful matching of 30 shaft parts and 30 hole parts after optimization, with an increase in average uniformity by 0.024. This highlights the proposed method’s superior effectiveness and accuracy in feature extraction and surface reconstruction.