Due to the lack of structure and part information in non-cooperative targets, the task of pose estimation suffers from unstable and unreliable initial coordinate system. In this paper, we introduce a curve-skeleton-based method to construct the robust coordinate system automatically for non-cooperative targets. First, a nonmanifold-Laplacian-based method is proposed to extract the curve skeleton from point clouds. The proposed method solves the over-contraction problem while preserves the topology and structure of skeleton well during point clouds contraction. Additionally, we create the skeleton graph to detect the skeleton structure and key points automatically. Then, the detected skeleton feature is used to construct target coordinate system, and improve the stability and robustness. Specifically, a real-scan dataset is constructed in this paper, and the proposed point cloud contraction method outperforms previous methods in structural representation and visualization. The mean rotation error of proposed coordinate system construct method performs 0.1249° and 1.2135° in 0%–30% noise ratio of distortions and outliers, and performs 7.04° and 4.21° in real-scan aircraft and satellite datasets. The results in complete and incomplete datasets verify the robustness and reliability of our skeleton-based coordinate system.