Restoring vegetation on waste dumps is imperative because soil erosion heavily impacts these areas and creates erosion micro-topographies, including bare slopes, rills, ephemeral gullies, and deposit bodies. These micro-topographies may affect seedling emergence by forming special micro-habitats, although the mechanism is vague. This study determined the substrate chemical (i.e., pH and electrical conductivity) and physical (i.e., capillary porosity, capillary water content, and mechanical composition) properties of different micro-topographies. In addition, the temporal dynamics of micro-climates (i.e., air temperature and air humidity), substrate hydrothermal conditions (i.e., substrate temperature and water content), and seedling emergence were investigated. Redundancy analysis (RDA), random forest (RF), and receiver operating characteristic (ROC) curve analysis were then used to identify the main factors affecting seedling emergence and clarify the relationships among the environmental conditions. Our results demonstrate that seedling densities in the rill, ephemeral gully, and deposit body were 1.78 times, 3.42 times, and 3.97 times higher than those on the bare slope, respectively. More species were found in the rill, ephemeral gully, and deposit body (Artemisia annua, Salsola collina, Setaria viridis, and Tribulus terrestris) than on the bare slope (Salsola collina). The main factors affecting seedling emergence were air humidity, substrate temperature, and substrate water content. The mechanical composition may have affected substrate water content during the initial stage of seedling emergence and substrate temperature during the entire period. We demonstrate that the ephemeral gully and deposit body may provide micro-habitats with a lower substrate temperature and higher substrate water content, which are favorable to seedling emergence, thus guiding vegetation restoration on waste dumps or other disturbed areas.