Biological soil crusts play significant roles in improving soil nutrients and ecological environment in arid and semi-arid area. To understand the effects of habitat diversity on the crust and surface soil, eight-year-old man-made algal crusts in Hopq Desert under Elymus dahuricus and Artemisia desterorum vegetation communities at four different topographical conditions: windward, peak, leeward and slack of the sand dune, were studied. The results showed that the crust biomass and soil available phosphorus were highest at the peak of the dune, reached to 4.24 mg/g and 2.926 mg/kg respectively, while total phosphorus and the activities of phosphatase and urease were highest at the dune slack. The crust biomass, soil available nitrogen, available phosphorus and the soil enzyme activity in the soil at the windward of the dunes were higher than those of the leeward obviously. At at the same topographical condition, the crust biomass, available nitrogen, available phosphorus, and the activities of phosphatase and urease in the surface soil under the Elymus dahuricus community were all higher than those of the Artemisia desterorum. The results indicated that the developing degree of the cultured algal crust had significant correlation with the surface soil nitrogen, phosphorus and soil enzyme activities. The habitat diversities resulted in different effects of the biological soil crust on the contents of nitrogen, phosphorus and the activities of soil enzymes, and different vegetation communities above the biological soil crusts produced different effects on the crust, generally the effects of the Elymus dahuricus community were higher than those of the Artemisia desterorum.