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Conversion of native desert into irrigated cropland is common in southern Taklimakan desert of China though the effect on soil fertility are not well understood. This study examined the effect of cultivation intensity on soil properties and crop productivity using 9-year data from cotton grown at three intensities of no fertilizer, low, and high fertilizer inputs. A native desert with sparse vegetation of Alhagi sparsifolia Shap. was used as a check. Treatment effects on soil properties fluctuated during 2005-2009 due to mineralization of applied manure or weather variation, and kept stable during 2010-2013. Soil organic carbon (SOC) during 2010-2013 increased with intensity, being 1.0-2.4 times greater in the fertilized than unfertilized cotton and desert. Soil total N, plant available N, and P content increased with fertilizer inputs. Available N content in the desert was 28.8mg kg(-1), being comparable to the low fertilizer treatment but approximately double that of unfertilized cotton, suggesting N fixing capacity of the leguminosae A. sparsifolia. Available K content was highest in desert and decreased with cultivation intensity. There were positive relationships between SOC and available N and P contents, suggesting SOC as a nutrient reservoir. Soil C:N ratio during 2010-2013 increased with intensity, being 8.7, 9.7, 10.8, and 12.0, for desert, no fertilizer, low, and high fertilizer input, respectively. Fertilizer application increased the 2010-2013 average cotton seed yield by 4.3-6.4 times compared to the unfertilized cotton field. In conclusion, our results suggest the intensive inputs of fertilizers are crucial to accelerate soil fertility and maintain the productivity of the recently converted lands from the desert.