In this paper, we propose a new approach for content-based video retrieval using non-parametric based motion classification in the shot-based video indexing structure. Our system proposed in this paper has supported the real-time video retrieval using spatio-temporal feature comparison by measuring the similarity between visual features and between motion features, respectively, after extracting representative frame and non-parametric motion information from shot-based video clips segmented by scene change detection method. The extraction of non-parametric based motion features, after the normalized motion vectors are created from an MPEG-compressed stream, is effectively fulfilled by discretizing each normalized motion vector into various angle bins, and by considering the mean, variance, and direction of motion vectors in these bins. To obtain visual feature in representative frame, we use the edge-based spatial descriptor. Experimental results show that our approach is superior to conventional methods with regard to the performance for video indexing and retrieval.