Hydraulic fracturing is a necessary method to develop shale gas reservoirs effectively and economically. However, the flow behavior in multi-porosity fractured reservoirs is difficult to characterize by conventional methods. In this paper, combined with apparent porosity/permeability model of organic matter, inorganic matter and induced fractures, considering the water film in unstimulated reservoir volume (USRV) region water and bulk water in effectively stimulated reservoir volume (ESRV) region, a multi-media water-gas two-phase flow model was established. The finite difference is used to solve the model and the water-gas two-phase flow behavior of multi-fractured horizontal wells is obtained. Mass transfer between different-scale media, the effects of pore pressure on reservoirs and fluid properties at different production stages were considered in this model. The influence of the dynamic reservoir physical parameters on flow behavior and gas production in multi-fractured horizontal wells is studied. The results show that the properties of the total organic content (TOC) and the inherent porosity of the organic matter affect gas production after 40 days. With the gradual increase of production time, the gas production rate decreases rapidly compared with the water production rate, and the gas saturation in the inorganic matter of the ESRV region gradually decreases. The ignorance of stress sensitivity would cause the gas production increase, and the ignorance of organic matter shrinkage decrease the gas production gradually. The water film mainly affects gas production after 100 days, while the bulk water has a greater impact on gas production throughout the whole period. The research provides a new method to accurately describe the two-phase fluid flow behavior in different scale media of fractured shale gas reservoirs.