In this article the mass and heat transfer between fluid molecule and carbon tube is studied via molecular dynamic simulation based on Lennard-Jones Potentia and Bernner-Tersoff Potential model. Some valve holes are formed by removing different numbers of molecules from flank of (5, 5) armchair carbon tube (the hole area = 17.3 ∼ 116.9Å2). The results indicate that only diffusion behavior is not able to describe the phenomena, otherwise the atom release rate and valve hole size are interdependent. Meanwhile the variation of potential energy barrier, work function, energy gap arose from different valve geometrical size are observed. These variations can influence the dynamic behavior such as flow rate and velocity by molecule penetration.