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Ammopiptanthus mongolicus is an ecologically important species in the arid region of Northwest China. Habitat disturbance can significantly affect plant mating success and ultimately species viability. Pollen limitation of plant reproduction occurs in many plant species, particularly those under habitat disturbance. However, previous investigations have demonstrated differences in pollen limitation between conserved and disturbed sites. We compared the phenology, pollen limitation, pollinators and breeding system of both sites to determine whether habitat disturbance has generated changes in these plant components. We found that the species differed in four aspects. First, blooming duration and flowering peak were longer in the disturbed site than in the conserved site. Second, A. mongolicus can be pollen-limited and pollen limitation was more intense in the conserved site than in the disturbed site. Third, Anthophora uljanini was found to be a frequent pollinator in the conserved site, while Apis mellifera was the most effective and frequent flower visitor. More pollinator visits were recorded in the disturbed site, which could explain the differences in reproductive success. Finally, seed set was higher in the disturbed site than in the conserved site. We found that outcrossing was dominant in both sites and that agamospermy and self-pollination played complementary roles to ensure reproduction. Differences in flower production influenced by artificial selection and pollinator type explain the different seed set in both sites, whereas habitat disturbance cause changes differences in the pollination process and limits pollen flow. The balance between artificial management and mating success is crucial to analysis of the pollination process and manipulation of A. mongolicus population size.