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As one of the best means of obtaining the geometry information of special shaped structures, point cloud data acquisition can be achieved by laser scanning or photogrammetry. However, there are some differences in the quantity, quality, and information type of point clouds obtained by different methods when collecting point clouds of the same structure, due to differences in sensor mechanisms and collection paths. Thus, this study aimed to combine the complementary advantages of multi-source point cloud data and provide the high-quality basic data required for structure measurement and modeling. Specifically, low-altitude photogrammetry technologies such as hand-held laser scanners (HLS), terrestrial laser scanners (TLS), and unmanned aerial systems (UAS) were adopted to collect point cloud data of the same special-shaped structure in different paths. The advantages and disadvantages of different point cloud acquisition methods of special-shaped structures were analyzed from the perspective of the point cloud acquisition mechanism of different sensors, point cloud data integrity, and single-point geometric characteristics of the point cloud. Additionally, a point cloud void repair technology based on the TLS point cloud was proposed according to the analysis results. Under the premise of unifying the spatial position relationship of the three point clouds, the M3C2 distance algorithm was performed to extract the point clouds with significant spatial position differences in the same area of the structure from the three point clouds. Meanwhile, the single-point geometric feature differences of the multi-source point cloud in the area with the same neighborhood radius was calculated. With the kernel density distribution of the feature difference, the feature points filtered from the HLS point cloud and the TLS point cloud were fused to enrich the number of feature points in the TLS point cloud. In addition, the TLS point cloud voids were located by raster projection, and the point clouds within the void range were extracted, or the closest points were retrieved from the other two heterologous point clouds, to repair the top surface and façade voids of the TLS point cloud. Finally, high-quality basic point cloud data of the special-shaped structure were generated.