The protection and management of the wetland should consider the changes in hydrological connectivity (HC) caused by the structural modifications of the soil macropores. The main purpose of our work is to clarify and quantify the influence of the soil macropores volume on the vertical soil hydrodynamic process mechanically and statistically by taking the form of a case study in Yellow River Delta (YRD), and further reveal the vertical hydrological connectivity in this area. Based on X-ray computed tomography and constant head permeability test, the results showed a highly spatial heterogeneity of the soil structure in the YRD, hydraulic parameter (K_s) was negatively correlated with bulk density and positively with soil macropore volume, soil aeration and maximum water capacity. Using Hydrus 1-D software and the Green–Ampt model, we estimated the characteristics of the hydrodynamic process in the soil without macropores, then evaluated the effect of the soil macropore on soil hydrodynamic process by comparing the experimental results with the simulation results. We found that increasing soil microporosity improved the convenience of water movement, which would enhance the HC of the region. The results will further help to reveal the eco-hydrological process at a vertical scale in soil and provide a theoretical guide for wetland conservation and restoration.