Supervoxel segmentation algorithm has been applied as a preprocessing step for many vision tasks. However, existing supervoxel segmentation algorithms cannot generate hierarchical supervoxel segmentation well preserving the spatiotemporal boundaries in real time, which prevents the downstream applications from accurate and efficient processing. In this paper, we propose a real-time hierarchical supervoxel segmentation algorithm based on the minimum spanning tree (MST), which achieves state-of-the-art accuracy meanwhile at least 11× faster than existing methods. In particular, we present a dynamic graph updating operation into the iterative construction process of the MST, which can geometrically decrease the numbers of vertices and edges. In this way, the proposed method is able to generate arbitrary scales of supervoxels on the fly. We prove the efficiency of our algorithm that can produce hierarchical supervoxels in the time complexity of O(n) , where n denotes the number of voxels in the input video. Quantitative and qualitative evaluations on public benchmarks demonstrate that our proposed algorithm significantly outperforms the state-of-the-art algorithms in terms of supervoxel segmentation accuracy and computational efficiency. Furthermore, we demonstrate the effectiveness of the proposed method on a downstream application of video object segmentation.