Snow and rainfall are two main water resources required for vegetation growth in the Gurbantunggut Desert, China. Epehmerals, an important component of plant community in this temperate desert in early spring, tend to be more sensitive to water availability than other types of plants. While previous studies mainly focus on the separate effects of snowpack or rainfall on the growth parameters of ephemerals, it is unclear, whether there is any interaction between snowpack and rainfall. Here an in-situ field experiment was conducted with snowpack and rainfall manipulation in the southern part of this desert. During two consecutive years, we measured ephemeral density, composition, and biomass under three snowpack and three rainfall treatments. The results indicated that snow and rainfall independently affected the variation in the density, composition, and productivity of ephemerals in this temperate desert. Increased depth of snow increased the ephemeral density in dry year but did not affect the species richness and productivity in both dry and wet years. However, rainfall significantly affected these parameters in the dry year, but had no dramatic effects in the wet year. Snowpack and rainfall differentially affect seedling establishment and productivity, and their effects are independent no matter in a dry or wet year.