The detection of the hole boundary of the point cloud model in reverse engineering is necessary for the hole repair, and a perfect hole contour line is conducive to improving the quality of the hole repair. Based on the definition of boundary in two-dimensinal images, the definition of hole boundary in three-dimensional point cloud was given. By analyzing the relationship between the eigenvalues of the covariance matrix of neighboring points, a boundary point detection operator was proposed to initially extract the feature points of the hole boundary, and then, the improved Kruskal minimum spanning tree algorithm was used to construct the minimum generated map of the point cloud. Subsequently, the hole boundary points were sorted and outline of the hole was extracted in the minimum generated graph. The experimental results show that the proposed boundary detection operator has simple steps and high efficiency. The hole contour line extracted by the hole contour line generation algorithm based on computer graph theory has the advantages of being smooth and continuous, and hole aggregation is completed while generating the contour line.