A skeleton matching method for 3D models of mechanical parts based on generalized transformation matrix was proposed. The connection line between the two skeleton points is called the skeleton branch. Referring to the representation method of the relationship between the generalized connecting rods in the robotics, the skeleton branches are regarded as a number of connecting rods. A fixed coordinate system and a skeleton coordinate system are established at the skeleton point. The skeleton branch is represented by the generalized transformation matrix. The generalized transformation matrix is transformed into a vector. Referring to the method of correlation measurement in statistics, the similarity degree of the two generalized transformation matrices was obtained by calculating the Pearson correlation coefficients of two vectors, that is, the similarity degree of the two skeleton branches. Search the matching skeleton branches and calculate the similarity of the whole skeleton. Through the example verification and experimental analysis, the algorithm has a fast retrieval speed and good accuracy.