Hydraulic fracturing has become a key technology to economically extract oil and gas from unconventional reservoirs. During hydraulic fracturing, fluid loss and water invasion into formation can cause serious permeability reduction near fracture face. At the same time, field practice also showed that well shut-ins after hydraulic fracturing could significantly increase hydrocarbon outputs, whereas the inner mechanism still remains unknown. In this paper, firstly, we studied permeability reduction after water invasion and permeability enhancement after well shut-ins using a core flooding system. Then, to investigate the inner mechanism, we studied aqueous phase migration during shut-ins using nuclear magnetic resonance (NMR) method. Results showed that fluids invasion reduce matrix permeability while well shut-ins can improve permeability and this improvement depends on the length of shut-ins time. NMR results showed that aqueous phases mainly distribute in macropores and mesopores after water invasion, while in shut-ins period, these invaded aqueous phases redistribute and migrate from larger pore spaces to smaller ones. Aqueous phase redistribution and migration during shut-ins period can remove near fracture water-block, reduce capillary discontinuity and increase the relative permeability of hydrocarbon phase, and this is the reason for permeability enhancement and hydrocarbon output increase after well shut-ins.