A novel approach for 3D motion capture data retrieval based on the Self-Organizing Map (SOM) and PCA index is proposed. Firstly, the Self-organizing map topological features are enhanced before learning. Characteristic will be mapped to a main surface after training every motion. Then, principal component analysis (PCA) is applied to deal with the surface characteristics. To improve the retrieval efficiency, an indexing scheme based on the principal eigenvector is constructed. Introduction of SOM avoid directing contact with the raw data, Follow-up work are only based on the main surface. It eliminate the position information influence of different frame length of the motion characteristics. Experimental results show that the algorithm is effective.