The tangential momentum and energy accommodation coefficients (TMAC and EAC) are parameters to characterize the velocity slip and temperature jump in the gas-solid interface. To understand the wall effects on fluid flow and heat transfer in nanochannels, the accommodation coefficients for argon gas molecules and platinum wall atoms were calculated according to a proper statistical algorithm using a three-dimensional molecular dynamic method. Isothermal flows and thermal conductions were simulated in smooth and rough nanochannels, in which the roughness ranged from 0.2 nm to 1.4 nm. From the atomic viewpoint, different lattice arrangements of smooth walls would induce atomic roughness to different extents on the surface, which affected the momentum and energy exchange in gas-wall interactions and resulted in different accommodation coefficients. In channels with nanoscale roughness, the possibility of multiple gas-wall interactions were further increased so that the TMAC and EAC became much larger with more roughness.