Non-rigid point cloud registration is a key component in many computer vision and computer graphics applications. The high complexity of the unknown non-rigid motion make this task a challenging problem. In this paper, we break down this problem via hierarchical motion decomposition. Our method called Neural Deformation Pyramid (NDP) represents non-rigid motion using a pyramid architecture. Each pyramid level, denoted by a Multi-Layer Perception (MLP), takes as input a sinusoidally encoded 3D point and outputs its motion increments from the previous level. The sinusoidal function starts with a low input frequency and gradually increases when the pyramid level goes down. This allows a multi-level rigid to nonrigid motion decomposition and also speeds up the solving by ×50 times compared to the existing MLP-based approach. Our method achieves advanced partial-to-partial non-rigid point cloud registration results on the 4DMatch/4DLoMatchbenchmark under both no-learned and supervised settings.