Biological soil crusts (BSCs) in arid region provide critical ecosystem services. However, most previous studies on BSC–plant topic have had a narrow spatiotemporal and taxonomic focus, so context dependency concerning exotic plant responses to BSCs remains poorly understood. In this study, using a series of manipulative experiments under greenhouse conditions, we investigated the influence of BSCs in the Tengger Desert in northern China on seed germination and seedling growth of an exotic grass species, Stipa glareosa P. Smirn., with or without two native plants species, Eragrostis poaeoides Beauv. and Artemisia capillaris Thunb., both of whose ontogeny differs from that of the exotic species. BSC treatments included intact crusts, disturbed crusts, and bare soil. Compared to bare soil, the presence of BSCs reduced the germination of E. poaeoides and A. capillaris by 78% and 74%, respectively. For the exotic species, BSCs reduced the germination percentage by as much as 90%. With gradual increases in soil nutrients such as organic carbon, available phosphorus, and available nitrogen, the shoot biomass of the three plants increased along the sequence from bare soil to lichens and mosses. Shoot biomass of the two native plant species was reduced by the exotic species S. glareosa. The percent germination and shoot biomass of S. glareosa on the disturbed crusts were greater than those on the intact crusts and bare soils. Overall, the presence of BSCs on stabilized sand dunes can reduce the germination of these three plant species, but compared with native plant species, BSCs have a stronger inhibitory effect on the seed germination of the exotic plant species. However, the disturbance may weaken the inhibition of the seed germination of the exotic grass S. glareosa and may provide more nutrients for the exotic grass S. glareosa to establish a revegetation region. We concluded that compared with the absence of BSCs, BSCs in this desert ecosystem can provide more nutrients and a suitable environment for native vascular plants and exert an inhibitory effect on the exotic plants.