Hydrogen-bond (H-bond) cross-linking has recently been proven a promising strategy for simultaneously improving strength, toughness, and ductility of H-bonded polymers. However, there has been a lack of an insightful understanding of how H-bond cross-linking works on a molecular level. To achieve understanding, coarse-grained (CG) simulation provides a possibility because of its high computational efficiency and access to longer lengths and time scales. However, existing coarse-grained force fields and potential functions exhibit an inability to accurately describe H-bonded polymer systems. Herein, we report a modified CG model to understand the H-bond crosslinking effect of small molecules, inositol (IN) in polyvinyl alcohol (PVA), with reference to MARTINI 3.0 parameters and empirical data. The simulation results show that incorporating IN results in a significant improvement in the strength, ductility, and toughness of PVA.which is in good agreement with experimental results. Moreover, the modified CG model establishes a close correlation between IN content, water content, tensile rate and glass transition, free volume, chain movement and mechanical properties of PVA. The results show that the yield strength of PVA initially increases and then decreases with the addition of IN. The maximum yield stress of PVA at IN-1.0 is approximately 155 MPa, representing a 33% increase compared to that of PVA. Additionally, the glass transition temperature (Tg) reaches 80.2 °C, ~2.8 °C higher than that of pure PVA. This work develops a modified CG model for understanding intermolecular interactions and mechanical properties of H-bonded polymer systems on a molecular level. This understanding is expected to help expediate the material design and properties optimization of strong and tough polymeric materials.