Large-scale molecular dynamics simulations are performed to study the effect of atomic-scale surface roughness on nano-contact. The modeling system consists of rigid spherical tips with different surface roughness and elastic flat substrate. Our results show that atomic-scale multi-asperity can change the contact behavior from consistent with the Hertz model to the Persson model. However, adhesion will reduce the influence of surface roughness, to the extent that the two tips with different roughness show similar variations of real contact area with applied load. The maximum compression and tensile stress of the rough tip is about 2 times and 1.5 times that of the smooth one, respectively. Moreover, the rough tip exhibits larger repulsive force and attractive force in the entire range of simulated load. Our simulations suggest that pull-off force cannot characterize the extent of the influence of adhesion on contact behavior at the nanoscale.