An Atomic-level model that can analyze the influence of the synthesis conditions (Molar ration, catalyst et al.) on the mechanical properties of phenol formaldehyde (PF) resins has been developed. This model clarified the relationship between synthesis conditions, the structure formation, and the structure-depended mechanical properties by introducing a comprehensive reaction model that includes both addition and condensation reactions. We validated the effectiveness of the model by verifying the influence of primary synthetic index, molar ratio, on the mechanical properties such as glass transition temperature (Tg) of resol resins. The computing cost has also been reduced since we adopted a multi-scale model which combined the Quantum chemistry calculation (QM), Monte Carlo (MC), and Molecular Dynamics (MD) method. This model will be helpful to reduce the cost of attempts at synthetic PF resins and more efficiently to find the suitable synthesis conditions for the desired material properties.