High‐confidence overlap prediction and accurate correspondences are critical for cutting‐edge models to align paired point clouds in a partial‐to‐partial manner. However, there inherently exists uncertainty between the overlapping and non‐overlapping regions, which has always been neglected and significantly affects the registration performance. Beyond the current wisdom, we propose a novel uncertainty‐aware overlap prediction network, dubbed UTOPIC, to tackle the ambiguous overlap prediction problem; to our knowledge, this is the first to explicitly introduce overlap uncertainty to point cloud registration. Moreover, we induce the feature extractor to implicitly perceive the shape knowledge through a completion decoder, and present a geometric relation embedding for Transformer to obtain transformation‐invariant geometry‐aware feature representations. With the merits of more reliable overlap scores and more precise dense correspondences, UTOPIC can achieve stable and accurate registration results, even for the inputs with limited overlapping areas. Extensive quantitative and qualitative experiments on synthetic and real benchmarks demonstrate the superiority of our approach over state‐of‐the‐art methods.