Establishing reliable correspondences is crucial for all registration tasks, including 2D image registration, 3D point cloud registration, and 2D-3D image-to-point cloud registration. However, these tasks are often complicated by challenges such as scale inconsistencies, symmetry, and large deformations, which can lead to ambiguous matches. Previous feature-based and correspondence-based methods typically rely on geometric or semantic features to generate or polish initial potential correspondences. Some methods typically leverage specific geometric priors, such as topological preservation, to devise diverse and innovative strategies tailored to a given enhancement goal, which cannot be exhaustively enumerated. Additionally, many previous approaches rely on a single-step prediction head, which can struggle with local minima in complex matching scenarios. To address these challenges, we introduce an innovative paradigm that leverages a diffusion model in matrix space for robust matching matrix estimation. Our model treats correspondence estimation as a denoising diffusion process in the matching matrix space, gradually refining the intermediate matching matrix to the optimal one. Specifically, we apply the diffusion model in the doubly stochastic matrix space for 3D-3D and 2D-3D registration tasks. In the 2D image registration task, we deploy the diffusion model in a matrix subspace where dual-softmax projection regularization is applied. For all three registration tasks, we provide adaptive matching matrix embedding implementations tailored to the specific characteristics of each task while maintaining a consistent "match-to-warp" encoding pattern. Furthermore, we adopt a lightweight design for the denoising module. In inference, once points or image features are extracted and fixed, this module performs multi-step denoising predictions through reverse sampling.