Non-rigid point cloud registration is a critical challenge in 3D scene understanding, particularly in surgical navigation. Although existing methods achieve excellent performance when trained on large-scale, high-quality datasets, these datasets are prohibitively expensive to collect and annotate, e.g., organ data in authentic medical scenarios. With insufficient training samples and data noise, existing methods degrade significantly since non-rigid patterns are more flexible and complicated than rigid ones, and the distributions across samples are more distinct, leading to higher difficulty in representation learning with few data. In this work, we aim to deal with this challenging few-shot non-rigid point cloud registration problem. Based on the observation that complex non-rigid transformation patterns can be decomposed into rigid and small non-rigid transformations, we propose a novel and effective framework, UniRiT. UniRiT adopts a two-step registration strategy that first aligns the centroids of the source and target point clouds and then refines the registration with non-rigid transformations, thereby significantly reducing the problem complexity. To validate the performance of UniRiT on real-world datasets, we introduce a new dataset, MedMatch3D, which consists of real human organs and exhibits high variability in sample distribution. We further establish a new challenging benchmark for few-shot non-rigid registration. Extensive empirical results demonstrate that UniRiT achieves state-of-the-art performance on MedMatch3D, improving the existing best approach by 94.22%.