With the widely application of hydraulic fracturing treatment, formation damage caused by fracture fluid invasion has become a thorny problem in unconventional gas reservoirs. Experiences in field operation indicate that shut-in the well for a period of time after hydraulic fracturing stimulation can reduce formation damage to some extent. Research indicates that the migration of fracture fluid from high water saturation zone to low water saturation zone is one of the key mechanisms to the mitigation of formation damage during shut-in period. However, an in-depth understanding about the aqueous phase migration between pores of different size during shut-in period is still lacking. In this study, unconventional gas reservoir rock samples were selected to simulate fracture fluid invasion and migration, nuclear magnetic resonance (NMR) technique was used to monitor the migration of aqueous phase in rock samples, and spontaneous imbibition experiments were conducted to investigate the imbibition characteristics of the samples. Results show that amplitude difference, vertex value, vertex position and peak width of T2 spectrum can be useful parameters to characterize the direction, speed and scope of the aqueous phase migration between pores of different size in rock samples. Aqueous phase migration between pores of different size has two stages: in first stage, aqueous phase migrates from small pores to large pores; in second stage, it migrates from large pores to small pores, which decreases the water saturation in large pores, and that is another important mechanism of formation damage mitigation during shut-in period. The duration and migratory volume of each stage are closely related to the pore characteristics and clay mineral content, and the duration of the two stages could help determine the proper occurrence and duration of the shut-in operation. Capillary force and osmotic pressure play important roles in the aqueous phase migration in pores, samples with highly developed micropores and high clay mineral content get a longer second stage, and a longer shut-in period is required to mitigate formation damage.