We describe a compression method for three-dimensional animation sequences that has notable advantages over existing techniques. We first aggregate the frame data by similarity and reorganize them into clusters, which results in the sequence split into several motion fragments of varying lengths. To minimize the number of clusters and obtain optimal clustering, we perform frame alignment, which eliminates the “global” rigid transformation from each frame data and use only “pose” when evaluating the similarity between frames. We then apply principal component analysis for each cluster, from which we get coordinates of corresponding frames in a reduced dimension. Because similar frames are considered, the number of coefficients required for each frame becomes smaller; thus, we obtain better dimension reduction for a given reconstruction error. Further, we perform intracluster compression based on linear coding. Because every motion fragment presents similar frames, conventional linear predictive coding can be replaced by key frame-based linear coding to achieve minimal reconstruction error. Results show that our method can obtain a high compression ratio, with a limited reconstruction error. Copyright © 2013 John Wiley & Sons, Ltd.