The invention relates to a method for reconstructing a large-scale complex flyover 3D model by using airborne LiDAR data. The method includes the following steps: using inverse iteration mathematic morphological filtering and area information to extract flyover point cloud from airborne LiDAR data; in accordance with bridge floor connectivity, segmenting the flyover cloud point; adopting a central line vertical line scanning method to segment and extract a communicated bridge surface which has no bifurcation or intersection structures and has a width consistent width, acquiring a "constitutional unit"; an end place of the constitutional unit central line serving as a circular buffer area, detecting a shielding structure of the flyover through determination of point cloud height information within the buffer area; through steps of constitutional unit matching, 2D central line fitting and 3D curved surface fitting, acquiring a complete bridge surface 3D central line; and reconstructing a flyover 3D model in combination with bridge surface width information. Practice has proved that the method of the invention can effectively reconstruct the large-scale complex flyover 3D model, addresses shielding problem of the flyover point cloud, and the reconstructed 3D model has a higher correctness and completeness.