3D scene flow estimation aims to estimate point-wise motions between two consecutive frames of point clouds. Superpoints, i.e., points with similar geometric features, are usually employed to capture similar motions of local regions in 3D scenes for scene flow estimation. However, in existing methods, superpoints are generated with the offline clustering methods, which cannot characterize local regions with similar motions for complex 3D scenes well, leading to inaccurate scene flow estimation. To this end, we propose an iterative end-to-end superpoint based scene flow estimation framework, where the superpoints can be dynamically updated to guide the point-level flow prediction. Specifically, our framework consists of a flow guided superpoint generation module and a superpoint guided flow refinement module. In our superpoint generation module, we utilize the bidirectional flow information at the previous iteration to obtain the matching points of points and superpoint centers for soft point-to-superpoint association construction, in which the superpoints are generated for pairwise point clouds. With the generated superpoints, we first reconstruct the flow for each point by adaptively aggregating the superpoint-level flow, and then encode the consistency between the reconstructed flow of pairwise point clouds. Finally, we feed the consistency encoding along with the reconstructed flow into GRU to refine point-level flow. Extensive experiments on several different datasets show that our method can achieve promising performance.