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Microbiotic crusts (MC), also called biological soil crusts or cryptogamic crusts, are formed by cyanobacteria, fungi, blue-green algae, lichens, and mosses, and are widespread in arid and semiarid zones such as the area of sands fixed in place by revegetation near Shapotou at the southeastern edge of China’s Tengger Desert. We studied mechanically disturbed and 40-year-old intact MC in this area using a series of soil hydrological experiments and ecological investigations to examine the ecohydrological responses after mechanical disturbance of the MC Once the MC was disturbed, the MC layer became ore primitive or disappeared entirely, resulting in a 32.8% decrease in the fine particles content of the upper soil layers, a 28.7% increase in soil albedo and a 168.9% decrease in the topsoil’s water-retention capacity. These changes greatly altered soil hydrological processes in the disturbed soils: the steady-state infiltration rates in the tipper soil layer increased by 693%, the precipitation recharge layer deepened, and the surface evaporation rate decreased by 20.3%. Moreover, the disturbance increased storage of plant-available water in the herbaceous rooting zone and improved the environment for germination and subsequent growth of annual herb species, as shown by a notable increase in the coverage, density, frequency, and biomass of annual plants. We conclude that MC represent a major component of Shapotou’s regional ecosystem and that disturbance will significantly alter local ecohydrological processes.