Soil enzymes actively participate in the nutrient transformation of soil system and are the key link between plants and soil nutrients. Soil enzyme activity is sensitive to the changes in rainfall patterns, particularly in deserts where rainfall is generally low and highly spatially and temporally variable. Little is known about how the timing and amount of rainfall affect soil nutrient contents and soil enzyme activity in areas where soil moisture is driven by snowmelt, particularly in early spring following complete snowmelt. We examined soil nutrient contents and enzyme activity at three times (Days 10, 20 and 30) and three rainfall amounts (5 mm, 10 mm, 15 mm) after complete snow melt, the period of maximum plant growth in the Gurbantunggut Desert in western China. We found no response under the lowest rainfall treatment (5 mm) at any times. The addition of 10 mm of rainfall stimulated a positive response in soil nutrients (e.g., nitrogen, phosphorus) but the 15 mm addition of rainfall had the greatest promotion effect on most soil indices such oxidase, phosphatase, and peroxidase activity, particularly 10 and 20 days after complete snow melt. Our results show that delaying of first rainfall time and addition of 15 mm rainfall after snowmelt can significantly increase soil microbial activity and nutrient transformation. These treatments can compensate for the inhibition effect of drought on nutrient transformation for a certain time period and enhance soil nutrients supply capacity in the growth period of desert ephemeral plants in early spring.