Enzymes play a crucial role as catalysts in biological processes, and enzyme therapy-utilizing biological enzymes-has gained significant attention for disease treatment. However, a critical challenge in enzyme therapy is the effective delivery of exogenous enzymes while maintaining their catalytic activity. Encapsulating enzymes in polymers offers a promising strategy to enhance their stability, prolong their half-life in the bloodstream, and improve biocompatibility. In this study, we employ dissipative particle dynamics (DPD) simulations combined with a reaction model to investigate the polymerization dynamics and the formation of a polymer nanocapsule around a nanoparticle that models an enzyme under mild reaction conditions. Our results show that the formation of a well-structured polymer nanocapsule depends on the strong attraction between monomers and the nanoparticle surface, low hydrophobicity, moderate polymerization rates, and weak chain stiffness. To optimize polymer nanocapsule preparation, we also examine the ratio of initiator to crosslinker at different monomer concentrations, identifying conditions that lead to a well-constructed polymer nanocapsule with high monomer participation. Our model is adaptable to various enzyme and monomer types by modifying their structures and properties, offering valuable insights for the future design of polymer nanocapsules in enzyme delivery.