To clarify the interaction between super-absorbent polymers (SAPs) and soil particles, and the influences of SAPs on soil structure and soil moisture availability under alternating dry and wet conditions, the soil column simulation experiments were carried out to study the effects of SAPs with different particle sizes (> 0.85, 0.6~0.85, 0.30~0.45 mm) on soil moisture characteristics, soil aggregate distribution and soil structure stability, and the microscopic changes of the valence bonds of SAPs and soil mixtures. The results showed that, compared with the control, the SAPs' treatments significantly increased the relative soil moisture content by more than 72.9% in the first (T1) and second (T2) sampling stages (P < 0.05), except for the minimum particle size treatment in T2 stage. The particle size of SAPs and soil moisture condition would affect the SAPs' application effect on soil water supply capacity. The SAPs with the smallest particle size had the poor ability to change the continuous soil water absorption and supply, but it had the most beneficial to promote the composition of soil water-stable macro-aggregates and the stability of soil aggregates. The interactions between SAPs and soil particles were intensified during continual soil wetting and drying cycles. The mineral colloids such as Si-O-Si bond, -OH, montmorillonite and quartz in the loam soil would enter into the network structure of SAPs, and the reaction intensity might affect the formation and stability of soil water-stable macro-aggregates. It was preliminarily analyzed that more soil clay minerals would destroy the molecular structure of SAPs during the process of repeated water loss and rehydration, which resulted in the decreases of the water absorption and holding capacities of SAPs.