Effect of atmosphere in ultra-micro cutting has been analyzed using MD (molecular dynamics) simulation carried out in such a way that potentials of surface atoms of diamond tool and silicon workpiece are modified when either of them is exposed to atmosphere. The results of the simulation show that principal cutting force decreases if the rake face of a tool and/or the rear face of chips are exposed to atmosphere during cutting. This result is consistent with the result obtained in microcutting experiments carried out by the authors and also indicates an important role of atmosphere in ultra-sonic vibration cutting.