Polymethyl methacrylate (PMMA)-based bone cement (BC) is a key material in joint replacement surgery that transfers external forces from the implant to the bone while allowing their robust binding. To quantitatively evaluate the effect of polymerization on the thermomechanical properties of the BC and on the interaction characteristics with the bone ceramic hydroxyapatite (HAp), molecular dynamics simulations were performed. The mechanical stiffness of the BC material under external loading increased gradually with the crosslinking reaction occurrence, indicating increasing load transfer between the constituent molecules. In addition, as the individual Methyl Methacrylate (MMA) segments were interconnected in the system, the freedom of the molecular network was largely suppressed, resulting in more thermally stable structures. Furthermore, the pull-out tests using HAp/BC bilayer models under different constraints (BC at 40% and 85%) revealed the cohesive characteristics of the BC with the bone scaffold in molecular detail. The stiffness and the fracture energy increased by 32% and 98%, respectively, with the crosslink density increasing.