We have conducted a long-term (from 1956 to 1999) rehabilitation experiment on mobile sand dunes in Tengger Desert, China, to investigate the chronological development of microbiotic soil crusts. We systematically analyzed the progression and development of the soil crusts by investigating the plant cover (herbs and shrubs), and some microorganism (mosses and algae), physical (particle size, saturated hydraulic conductivity and saturated water content) and chemical (major plant nutrients and organic matter) soil particles. The Limburg Soil Erosion Model was used to simulate infiltration and runoff. Three stages of microbiotic crust development occurred during the progressive stabilization of unconsolidated aeolian dunes, from 1956 to the present day: (1) raindrop impact and development of a non-biological crust; (2) crust enriched with mosses; (3) crust dominated by abundant algae, mosses and liverworts. It is considered that the most significant driving factor in the ecological development of microbiotic crusts in the Tengger Desert is the spatial variability of rainfall infiltration depth within the various soil layers occurring on, for example, dune top, leeward slopes, inter-dune depression (hollow) and windward slopes, immediately after a single individual rainfall event. Crust development leads to a change from shrubs to herbs because of decreased soil moisture in deeper soil layers.