Soil seed banks (SSBs) serve as the fundamental basis for natural vegetation regeneration, and their relationship with aboveground vegetation (AV) plays an important role in achieving natural rehabilitation of wetlands. Grazing is the predominant form of wetland resource utilization in semi-arid regions, significantly influencing biodiversity and ecological functions. Although the response of wetland SSBs to grazing is an important focus area in ecology research and microtopography is extremely common in semi-arid wetlands, the mediating role of microtopography in regulating the impact of herbivores on SSB dynamics remains unclear. To address this knowledge gap, this long-term field study (2000-2023) investigated the effects of four grazing intensities (no, slight, moderate, and heavy grazing) and three microtopographic conditions (hummock apex, hummock brae, and hummock interspace) on SSBs. Results revealed that the interaction between grazing and microtopography significantly influenced SSBs and their association with AV. The density and richness of SSBs decreased with an increase in grazing intensity and significantly varied with microtopographic heterogeneity. The similarity between SSBs and AV initially increased and subsequently decreased with increasing grazing intensity, with the similarity level being higher for the hummock apex than for other positions. Electrical conductivity (EC), total dissolved solid levels, and nitrate nitrogen (NO3--N) levels were significantly negatively correlated with the density and richness of SSBs and the density of AV. Redundancy analysis indicated that EC and NO3--N significantly influenced SSB properties across all grazing intensities, and that EC was a key driver of changes in the structural attributes of AV. Furthermore, a structural equation model indicated that grazing and micro-topography directly affected SSB properties. In particular, microtopography mediated the process through which grazing disturbed AV, thereby affecting SSBs. Altogether, these findings suggest that grazing and micro-topography profoundly affect the structural attributes of wetland SSBs through multiple pathways. These findings enhance the understanding of the ecological functions of microtopography and provide valuable insights into the near-natural restoration and sustainable utilization of grazed wetland ecosystems.