Spatial variation of riverbed topography caused by the difference of dynamic conditions of surface water affects spatial distribution of pressure at water-sediment interface, which has an important influence on the interaction between surface water and groundwater and the interaction between groundwater and wetland water. To reveal the influence mechanism of riverbed undulations on surface water-ground water interaction, This study established a groundwater flow numerical simulation model and analyzed the influence mechanism of riverbed topography on surface water-groundwater-wetland interaction process based on the characteristics of riverbed topographic undulations of a profile at Liuyuankou, Kaifeng, the lower reaches of the Yellow River. The results show that: (1) compared with flat riverbed, the variable riverbed topography leads to an increasing exchange fluxes between surface water and between groundwater and wetland water; (2) The spatial fluctuation of riverbed topography forms different levels of groundwater flow systems at the bottom of the riverbed, and changes the groundwater flow path and the travel time. Compared with the flat bed topography, the variation of the topography of river bed complicates the groundwater flow path in the underlying aquifer. Retention areas are developed in different positions in the aquifer near the bed interface. Moreover, the greater topography degree of the river bed, the older the groundwater age in the aquifer beneath the wetland bed and aquifer near the wetland. This study can provide theoretical basis for promoting the coordinated protection of surface water, groundwater and wetland water in the suspended reach of the lower Yellow River.