Abstract Gas flow in nanoporous rocks is closely relevant to several globally important energy and environmental issues, such as shale-gas production and CO2 subsurface sequestration. The Klinkenberg effect is critical to an understanding of gas flow, yet many specifics are unclear for nanoporous rocks. Here we investigated gas flow and the Klinkenberg effect in nanoporous rocks on the basis of a systematic study of gas permeability and diffusivity under a range of pore pressures and varying water saturations. We invalidated the use of the Klinkenberg equation for determination of intrinsic permeability and the Klinkenberg slippage factor on the basis of measurements in current laboratory conditions and propose a modified Klinkenberg equation for a more reliable determination of the slippage factor. We show that gas relative permeability is higher at higher pore pressures and that the Klinkenberg effect is more important in lower water saturations than in higher ones. The underlying mechanism of increased pore size after saturation was elucidated through neutron imaging on water distribution. In addition, we demonstrate that gas diffusivity better characterizes the diffusive gas flow than gas permeability and can be higher at higher pressures in either dry or partly saturated conditions. Finally, a characteristic pore-diameter index was derived on the basis of a new form of porosity–permeability relationship and was found to have a good correlation, which was previously lacking, with the Klinkenberg slippage factor for nanoporous rocks. Collectively, these new insights can advance the understanding of gas flow in nanoporous rocks and will have important implications on industrial applications.