<p>Here we introduce a framework for molecular structure optimization using a denoising model on a physics-informed Riemannian manifold (R-DM). Unlike conventional approaches operating in Euclidean space, our method leverages a Riemannian metric that better aligns with molecular energy change, enabling more robust modeling of potential energy surfaces. By incorporating internal coordinates reflective of energetic properties, R-DM achieves chemical accuracy with an energy error below 1 kcal mol⁻¹. Comparative evaluations on QM9, QM7-X and GEOM datasets demonstrate improvements in both structural and energetic accuracy, surpassing conventional Euclidean-based denoising models. This approach highlights the potential of physics-informed coordinates for tackling complex molecular optimization problems, with implications for tasks in computational chemistry and materials science.</p>