Infiltration and soil water content (SWC) are key concerns to agro-hydrological researchers. Understanding of irrigation-induced infiltration and soil water characteristics are fundamental to irrigation management and improving agricultural Water Use Efficiency (WUE) in arid and semi-arid areas. Based on measurements from a test site in Xinjiang, China, numerical simulations have been performed to investigate the infiltration processes under alternating drip irrigation operations. The present study focuses on simulating infiltration physics and analyzing its potential impacting factors, to shed light on the design of irrigation systems that improve WUE. The results show that irrigation schedules, surface sealing, residual water saturation, and soil fractures have significant impacts on SWC patterns for both the irrigation durations and intermittences. Low frequency irrigation with high watering rates should be avoided due to its low irrigation efficiency. Commencing with lower-rate irrigation is probably the best practice for efficient irrigation for shallow-root crops. The soil infiltrability drops exponentially or polynomially with the decrease in permeability of the immediate surface. Introduction of a 5-mm soil surface seal with a permeability of 5 mD leads to about 97.1% reduction in the infiltrability. Residual water saturation Swr or water content has positive correlations with Volumetric soil Water Content (VWC), due to the trapping of the residual water. Enhancement of one-fold magnitude of Swr causes 6.12% and 20.4% higher VWC for the loamy sand, but 7.57% and 5.71% lower VWC for the underlying sandy loam, at the 160 hr and 720 hr respectively. The presence of soil fractures leads to apparent preferential flows in the soil, which cause the wet fronts to penetrate to 115.9% and 53.88% deeper depths at the 160 hr and 720 hr, respectively.