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Calligonum mongolicum is a successful pioneer shrub to combat desertification, which is widely used for vegetation restoration in the desert regions of northwest China. In order to reveal the limitations to natural regeneration of C.mongolicum by asexual and sexual reproduction, following the process of sand dune stabilization, we assessed clonal shoots, seedling emergence, soil seed bank density, and soil physical characteristics in mobile and stabilized sand dunes. Controlled field and pot experiments were also conducted to assess germination and seedling emergence in different dune soil types and seed burial depths. The population density of mature C.mongolicum was significantly different after sand dune stabilization. Juvenile density of C.mongolicm was much lower in stabilized sand dunes than mobile sand dune. There was no significant difference in soil seed bank density at three soil depths between mobile and stabilized sand dunes, while the emergence of seedlings in stabilized dunes was much lower than emergence in mobile dunes. There was no clonal propagation found in stabilized dunes, and very few C.mongolicum seedlings were established on stabilized sand dunes. Soil clay and silt content, air-filled porosity, and soil surface compaction were significantly changed from mobile sand dune to stabilized dunes. Seedling emergence of C.mongolicm was highly dependent on soil physical condition. These results indicated that changes in soil physical condition limited clonal propagation and seedling emergence of C.mongolicum in stabilized sand dunes. Seed bank density was not a limiting factor; however, poor seedling establishment limited C.mongolicum’s further natural regeneration in stabilized sand dunes. Therefore, clonal propagation may be the most important mode for population expansion in mobile sand dunes. As a pioneer species C.mongolicum is well adapted to propagate in mobile sand dune conditions, it appears unlikely to survive naturally in stabilized sand dune plantations.