The near-surface weathered granitic soil (WGS) is easily affected by cyclic drying and wetting due to seasonal alterations. The microstructural damage was characterized using the technology of nuclear magnetic resonance (NMR) imaging and mercury intrusion porosimetry (MIP) to study the influence of dry and wet seasons impacts on microstructures of soils. The results revealed that the relaxation time (T2) spectrums from NMR investigation were strongly affected by multiple wetting-drying cycles, and the porosity had a positive nonlinear relationship with the peak areas. As implied in the MIP and NMR analysis, PSD curves of WGS were characterized by bimodal distributions as the pore diameter in two peaks ranging from 0.1 μm to 5 μm and 5 μm ~100 μm, respectively. As the number of cycles increases, the left peak of the PSD curve successively shifts downwards while the right peak shifts upwards, implying that a large number of small-sized micro-pores in the WGS gradually expand and connect to macro-pores. Under the influence of periodic water migrations in soils, the areas of bright spots in the T2-weighted images increased, reflecting that the structural damage degree was accelerated with continued enlargement of internal pores. Through a comparison between NMR-based and MIP-based PSDs, NMR can better capture more accurate information on the pore distribution attributed to its advantage of test principle and nondestructive scanning. The process of cyclic wetting and drying severely reformed the microstructure of the WGS, causing the micropores to gradually expand to form macropores and thus deteriorating the soil microstructure.