Mass and heat transfer between fluid molecules and a carbon tube is studied via molecular dynamic simulation with Lennard-Jones potential and Bernner-Tersoff potential. A valve hole of area 17.3~116.9Å2 is formed by removing different numbers of molecules from the flank of a (5,5) armchair carbon tube. The results indicate that diffusion behavior can not describe the phenomena completely, since the hydrogen atoms penetration rate Vb can also be affected by hole size at the same temperature. The Maxwell-Bohzmann energy distribution equation is modified. Atom release rate and valve hole size are interdependent. Variation of potential energy barrier, work function and energy gap at different valve sizes and influences on the dynamic behavior, such as flow rate and velocity by molecule penetration, are studied. The characteristic is used for design of nano-valve, particle separator or chemical reactor.