The main phase transition temperature of a lipid membrane, which is vital for its biomedical applications such as controllable drug release, can be regulated by encapsulating hydrophobic nanoparticles into the membrane. However, the exact relationship between surface properties of the encapsulating nanoparticles and the main phase transition temperature of a lipid membrane is far from clear. In the present work, we performed coarse-grained molecular dynamics simulations to meet this end. The results show the surface roughness of nanoparticles and the density of surface-modifying molecules on the nanoparticles are responsible for the regulation. Increasing the surface roughness of the nanoparticles increases the main phase transition temperature of the lipid membrane, whereas it can be decreased in a nonlinear way via increasing the density of surface-modifying molecules on the nanoparticles. The results may provide insights for understanding recent experimental studies and promote the applications of nanoparticles in controllable drug release by regulating the main phase transition temperature of lipid vesicles.