The Sponge City construction currently undergoing in China aims to enhance the moisture capacity of urban pedosphere, and subsurface moisture content (SMC) is proposed to evaluate the effect of improvement. Different ground-penetrating radar (GPR) techniques have been used in previous studies to estimate moisture content, however, very few has assessed the potential of combing 2D common offset (CO) GPR with 3D multichannel GPR to resolve SMC estimates at the complex filed scale. In this paper, modified velocity analysis of in-situ 3D GPR common-midpoint (CMP) datasets was used together with 2D GPR laboratory calibration procedure to investigate spatial moisture variation and the impact of surface pavement and soil heterogeneity on subsurface water dynamics. Precise and reliable moisture information under two field sites (i.e., sponge pavement site and asphalt pavement site) was obtained, which further allowed us to quantitative characterize SMC distribution and its associated dynamics within the shallow vadose zone, and most importantly to investigate the coupling mechanism between subsurface water fluctuations with surface pavement conditions and subsoil moisture capacity in urban near surface environment. Additionally, through contrastive analysis, the superior performance of novel sponge material to detain and transit rainwater was highlighted. Data and results presented in this research provide pioneer reference for Sponge City construction and other engineering applications.