Molecular Dynamics (MD) simulations are vital for predicting the physical and chemical properties of molecular systems across various ensembles. While All-Atom (AA) MD provides high accuracy, its computational cost has spurred the development of Coarse-Grained MD (CGMD), which simplifies molecular structures into representative beads to reduce expense but sacrifice precision. CGMD methods like Martini3, calibrated against experimental data, generalize well across molecular classes but often fail to meet the accuracy demands of domain-specific applications. This work introduces a Bayesian Optimization-based approach to refine Martini3 topologies—specifically the bonded interaction parameters within a given coarse-grained mapping—for specialized applications, ensuring accuracy and efficiency. The resulting optimized CG potential accommodates any degree of polymerization, offering accuracy comparable to AA simulations while retaining the computational speed of CGMD. By bridging the gap between efficiency and accuracy, this method advances multiscale molecular simulations, enabling cost-effective molecular discovery for diverse scientific and technological fields.