Imbibition controls mass transfer in the complex pore-fracture network in shale, which may change the pore-fracture network and lead to a low efficient flowback of fracturing fluid. Thus, it is necessary to accurately characterize the pore-fracture network alteration during the imbibition process. In this study, forced and spontaneous imbibition tests were conducted under the confining pressure on selected shale core samples with induced fractures, collected from Longmaxi Formation, Sichuan Basin, China. The low-field nuclear magnetic resonance (NMR) spectrometer was employed to monitor the variation of pores and micro-fractures in the shale core samples during the dynamic imbibition process. In addition, optimal surface relaxivities, ranging from 0.019 to 0.033 μm/ms, were determined by comparing the NMR T2 distributions with the pore size distributions (PSDs) measured via high-pressure mercury intrusion (HPMI) tests. Then, the measured dynamic T2 spectra with three distinct peaks were converted into the corresponding PSDs to quantitatively analyze the number, size, and connectivity changes of small pores, large pores, and micro-fractures in shale. Results show that the total porosities of the four shale core samples are increased by 3.5%, 10.2%, 32.9%, and 36.3% after the imbibition tests. The forced imbibition leads to more remarkable improvements in the pore volume of large pores with radius between 0.2 and 3.6 μm. In contrast, the spontaneous imbibition results in more significant increases in the number and size of small pores with radius between 0.0004 and 0.36 μm. It is also found that the total porosity increment is primarily an outcome of small pore alteration during the imbibition. Moreover, the enlarged pores and micro-fractures are mainly categorized as the capillary bounded fluid pores and movable fluid pores, which significantly affect the efficiency of oil and gas transfer in shale. The findings of our study demonstrate the comprehensive effects of capillary force, clay hydration, osmotic potential, confining and pore pressures, and creep deformation and failure on the pore-fracture network alteration in shale and advance the understanding of the mechanisms behind the forced and spontaneous imbibition processes.