Hydraulic fracturing has been recognized as the necessary well completion technique to achieve economic production from shale gas formation. However, following the fracturing, fluid–wall interactions can form a damaged zone nearby the fracture characterized by strong capillarity and osmosis effects. Here, we present a new reservoir multi-phase flow model which includes these mechanisms to predict formation damage in the aftermath of the fracturing during shut-in and production periods. In the model, the shale matrix is treated as a multi-scale porosity medium including interconnected organic, inorganic slit-shaped, and clay porosity fields. Prior to the fracturing, the matrix holds gas in the organic and the inorganic slit-shaped pores, water with dissolved salt in the inorganic slit-shaped pores and the clay pores. During and after fracturing, imbibition causes water invasion into the matrix, and then, the injected water–clay interaction may lead to clay-swelling pressure development due to osmosis. The swelling pressure gives additional stress to slit-shaped pores and cause permeability reduction in the inorganic matrix. We develop a simulator describing a system of three pores, two phases (aqueous and gaseous phases), and three components (H 2O , CH 4, and salt), including osmosis and clay-swelling effect on the permeability. The simulation of aqueous-phase transport through clay shows that high swelling pressure can occur in clays as function of salt type, salt concentration difference, and clay-membrane efficiency. The new model is used to demonstrate the damage zone characteristics. The simulation of two-phase flow through the shale formation shows that, although fracturing is a rapid process, fluid–wall interactions continue to occur after the fracturing due to imbibition mechanism, which allows water to penetrate into the inorganic pore network and displace the gas in-place near the fracture. This water invasion leads to osmosis effect in the formation, which cause clay swelling and the subsequent permeability reduction. Continuing shale–water interactions during the production period can expand the damage zone further.