Multiple flow mechanisms that coexist in nanoscale porous media are responsible for deviations from the linear Klinkenberg equation. The use of mathematical models in the literature has obvious limitations in evaluating this flow phenomenon because the viscosity/diffusion coefficients of nanoscale porous media are more accurate only in the limited Knudsen number region. By introducing, the concept of an effective molecular mean free path, this paper proposes single models of viscosity/diffusion for the full Knudsen number range to replace the combination model in the literature. On this basis, a new apparent permeability model is developed with multiple coexisting mechanisms for the full Knudsen number range, and the effectiveness of the proposed model is verified by using published data. The discontinuous problem of the combination model of the viscosity/diffusion coefficient in the literature for the full Knudsen number range is solved using the new viscosity and diffusion coefficient models. The new apparent permeability model accurately predicts the absolute permeability and explains the phenomenon of deviation from the linear Klinkenberg equation. This paper further discusses the influence of different mechanisms on the permeability. The rarefaction effect weakens the diffusion ability in porous media but increases the contribution of Darcy flow to permeability. The viscous flow increment, absolute permeability and slippage effect were the most important flow mechanisms in nanopores.