Shale can act as an unconventional gas reservoir with low permeability and complex seepage characteristics. Study of the apparent permeability and percolation behavior of shale gas is important in understanding the permeability of shale reservoirs, to evaluate formation damage, to develop gas reservoirs, and to design wells. This study simulated methane percolation at 298.15 K under inlet pressures ranging from 0.2 to 4 MPa and a constant outlet pressure of 0.1 MPa to investigate shale gas percolation behavior and apparent permeability. Five representative shale cores from the Carboniferous Hurleg and Huitoutala formations in the eastern Qaidam Basin, China, were analyzed. Each experiment measured the volume flow rate of methane and the inlet pressure. Pseudopressure approach was used to analyze high-velocity flow in shale samples, and apparent permeability at different pressures was calculated using the traditional method. A nonlinear apparent permeability model that considers diffusion and slippage is established from theory and experimental data fitting, and the shale gas flow characteristics affected by slippage and diffusion are analyzed. The results indicate that the pseudopressure formulation that considers the effect of gas properties on high-velocity flow produces a more accurate linear representation of the experimental data. The apparent gas permeability of shale consists of contributions from Darcy permeability, slippage, and diffusion. The apparent permeability and gas flow behavior in the studied shales strongly depended on pressure. The diffusion contribution increased greatly as pressure decreased from 2 to 0.2 MPa, and the smaller the shale permeability, the greater the relative contribution of diffusion flow. At pressures greater than 2 MPa, slip flow contributes 20% of the total flux, Darcy flow contributes up to 70%, and diffusion makes only a minor contribution. This study provides useful information for future studies of the mechanism of shale gas percolation and the exploration and development of Qaidam Basin shale gas specifically.