Shale gas is a very important energy resource for humans in the 21st century. However, the mechanism underlying the transoport behavior of shale gas in nanopores (typically 1 nm to 100 nm) remains a huge challenge in industries, as well as in research. In this study, we investigated the free gas transport in nanopores of shale rocks by using the real gas equation of state (EOS) and elastic hard-sphere (HS) model. Excellent results were obtained from the validation of the real gas model on the basis of molecular simulation and experimental data. This paper discusses the following: (1) the model efficiently and reasonably describes the known gas transport behavior in nanopores by establishing the relationship among real gas effect, molecular interactions and collisions, and gas transport behavior; (2) the use of real gas HS EOS considers repulsion, which reduces Knudsen diffusion and laminar slip flow conductance. In addition, packing fraction in EOS provides minimum boundaries for Knudsen number and flow regime; (3) the molecule-wall collision is mainly dominated by pore diameter, and the intermolecular collision is mainly dominated by pressure in nanopores. Under 10 MPa, the molecule-wall collision dominates in nanopores. Otherwise, the intermolecular collision dominates; (4) the laminar slip flow conductance increases with the corresponding increase in strength of intermolecular collision. With increased strength in the molecule-wall collision, Knudsen diffusion conductance increases, thereby improving the transport efficiency, as shown by apparent permeability.