In real-world applications, data often reside in restricted domains with unknown boundaries, or as high-dimensional point clouds lying on a lower-dimensional, nontrivial, unknown manifold. Traditional Gaussian Processes (GPs) struggle to capture the underlying geometry in such settings. Some existing methods assume a flat space embedded in a point cloud, which can be represented by a single latent chart (latent space), while others exhibit weak performance when the point cloud is sparse or irregularly sampled. The goal of this work is to address these challenges. The main contributions are twofold: (1) We establish the Atlas Brownian Motion (BM) framework for estimating the heat kernel on point clouds with unknown geometries and nontrivial topological structures; (2) Instead of directly using the heat kernel estimates, we construct a Riemannian corrected kernel by combining the global heat kernel with local RBF kernel and leading to the formulation of Riemannian-corrected Atlas Gaussian Processes (RC-AGPs). The resulting RC-AGPs are applied to regression tasks across synthetic and real-world datasets. These examples demonstrate that our method outperforms existing approaches in both heat kernel estimation and regression accuracy. It improves statistical inference by effectively bridging the gap between complex, high-dimensional observations and manifold-based inferences.