Computational model for AFM using the coupling method of molecular dynamics (MD)and continuum is proposed in order to investigate mechanism of the observed energy dissipation in AFM. The motion of cantilever is described by a spring, and the atomic interaction between the tip attached on cantilever and surface is calculated by MD method. The motions of the spring and atoms are coupled by the MD/continuum hybrid method. We find that a significantly energy dissipation comes from atomic thermal fluctuation between the tip and surface. To further study this dissipation mechanism, the temperature and frequency dependence of the dissipation is investigated.