Hydraulic fracturing is widely applied for economical gas production from shale reservoirs. Still, the swelling of the clay micro/nano pores due to retained fluid from hydraulic fracturing causes a gradual reduction of gas production. Four different gas-bearing shale samples with different mineralogical characteristics were investigated to study the expected shale swelling and reduction in gas permeability due to hydraulic fracturing. To simulate shale softening, these shale samples were immersed in deionized (DI) water heated to 100 °C temperature and subjected to 8 MPa pressure in a laboratory reactor for 72 hours to simulate shale softening. The low-temperature nitrogen adsorption and density measurements were performed on the original and treated shale to determine the changes in micro and nano pore structure. The micro and nano pore structures changed, and the porosity decreased after shale treatment. The porosity decreased by 4% for clayey shale, while for well-cemented shale the porosity only decreased by 0.52%. The findings showed that the initial mineralogical composition of shale plays a significant role in the change of micro and nano pores and the pore structure alteration due to retained fluid from hydraulic fracturing. A pore network model is used to simulate the permeability of shale used in this study. To define pore structure properties, specific factors such as porosity, pore size, pore throat distribution, and coordination number were used. Furthermore, the anisotropy characteristics of shale were integrated into the model via a coordination number ratio. Finally, the change in permeability due to shale softening was determined and compared with untreated with the progress of shale softening. The simulation showed that the permeability of Longmaxi shale could decrease from 3.82E–16 m2 to 4.71E–17 m2 after treatment.