Cryogenic pumps are convenient machinery for handling hydrogen isotopes in fusion fuel processing systems. Not only ultra-vacuum pumps working at such as liquid helium or hydrogen temperature but also sorption pumps using liquid nitrogen are applicable. The latter type is suitable to a means of temporary storage and/or transportation between process units. In the cryogenic pumping, there is an issue that the pressure in a pump is not necessarily identical with the pressure measured in its evacuating vessel in equilibrium, because of an effect of thermal transpiration. Thermal transpiration is important in adsorption isotherms which characterize cryo-sorption pumping. In this study, the effect of thermal transpiration was investigated for He, H2 and D2 in a closed system consisting of a volume at room temperature and a volume at cryogenic temperature, connected together by a simple narrow pipe or a pipe containing baffle plates as thermal shield. The effect is here described by an equation of nominal-distribution function with respect to the pressure measured in the hot end volume. Defining an effective inner diameter for the latter pipe, agreement is shown of characteristic curves for geometrically different pipes. The error-functional curves for H2 and D2 are agreed together. The curve for He is also perfectly approximated but with a constant shift. This shift results in the difference of a molecular property among He, H2 and D2.