Understanding the interactions of nanoparticles (NPs) with biological system, especially interactions with cell membranes, is critical for the rational design of nanocarrier agents and drug delivery systems. Here, we have performed coarse-grained molecular dynamics simulations aimed at the effect of hydrophilic/hydrophobic properties of nanoparticles on the interaction with cell membranes (dipalmitoylphosphatidylcholine or DPPC bilayer). Two kinds of nanoparticles (hydrophobic and semihydrophilic) are modeled in the simulation. The results indicate that a hydrophobic nanoparticle can result in the inclusion into the bilayer, whereas a semihydrophilic nanoparticle is only found to adsorb into the membrane. For different system free energy profiles have been calculated to elucidate those phenomena. For the semihydrophilic nanoparticle case, we also discuss the potential substantial energy barrier of particle wrapping, implicating that the endocytosis-like mechanism is an energy-mediated process. The landscapes of the membrane fluctuation in the transitions imply that the deformation of the lipid bilayer induced by the addition of NPs is short-range, and the rearrangement of lipid molecules plays a significant role for morphological variations of NP-containing lipid membrane patches. These results show that the surface hydrophobicity can result in different response mechanisms of NP-biomembrane interactions.