The study sheds important light on how polymer nanoparticles—more especially, polystyrene interacts with biological membranes. The polystyrene behavior in lipid bilayers was successfully assessed using both MARTINI Coarse-Grained and All-atom CHARMM36 force fields, demonstrating the influence of cholesterol on membrane dynamics and polystyrene integration. The stability of polystyrene's insertion into the DPPC membrane, as well as cholesterol's impact on membrane arrangement, highlight how intricate these interactions are. Moreover, the results concerning PS conformational flexibility, especially when cholesterol is present, provide insight into the complex dynamics of polystyrene in the membrane environment.