According to the requirement of digital assembly for large aeronautical components, a mobile robot machining system for milling and drilling on the docking surface is designed, and the specific machining process is proposed. The preprocessing algorithm of large amount of scattered point cloud data based on laser scanner is studied. A feature extraction algorithm of docking surface based on raster method and iterative fitting method is proposed. Aiming at the problem of high precision positioning of mobile robot machining system in large scene, a coordinate alignment algorithm of docking reference hole based on scanning line method and least square method is proposed. Through the machining experiment verification of aeronautical component, the accuracy of milling and drilling meets all the technical indicators of the system requirements, and proves that the mobile robot milling and drilling system proposed in the paper can accurately complete the digital assembly task of large aeronautical components, and has important significance for improving assembly quality and efficiency.