The invention discloses a method for preventing water erosion desertification by using biological crust, which is to artificially inoculate a biological crust resource onto bare soil surface of a water erosion desertified area and cultivate the biological crust to allow the biological crust to cover the bear soil surface. The method comprises the following steps:1) selecting well developed natural biological crust, and shoving 10 to 30-millimeter-thick crust layer on surface for later use; 2) drying the collected biological crust in shade, removing other materials, crushing, fully stirring and uniformly mixing to obtain the biological crust resource; 3) mixing the prepared biological crust resource with fine soil according to a ratio of 1:(1-2), uniformly spreading the mixture on the soilsurface to be inoculated, covering a small amount of fine soil, and fully watering after the fine soil is covered; and 4) controlling a proper condition to promote the growth of the biological crust,namely watering, topdressing, killing pests and weeding. With the method of artificial inoculation and cultivation, a high-coverage biological crust can be formed in a short period, and the formed biological crust has obvious water and soil holding function; and the method is an effective method for treating water erosion desertification.