Ephemeral plants are a unique part of desert flora. They are mainly distributed in the Junggar Basin and are of great importance to the stability of dunes in the Gurbantünggüt Desert. However, quantitative information on the relationship between precipitation and ephemeral plant distribution remains poorly studied. In 2009, 2011, and 2012, ephemeral plants in 73 plots located on the southern edge of Gurbantünggüt Desert were investigated. Using ArcGIS 10.0 software, daily precipitation data of each plot were obtained by spline interpolation at 0.05° resolution from daily realtime gridded precipitation data of China. Using richness and coverage of ephemeral plants as the dependent variables, and precipitation during the growth period, season and month as independent variables, stepwise multivariate linear regression and principal component analysis were conducted to determine the effects of different precipitation types on the distribution of ephemeral plants and on the distribution of ten widespread and ten rare species. Results indicated that the richness of ephemeral plants was correlated with precipitation in spring, leaf expansion period, and May (classified according to different criterions), while their coverage was correlated with precipitation in spring, fruiting period and May. Precipitation in May and June had a significant impact on the widespread species, and precipitation in March, April, May and July had a significant impact on the rare species. Altogether, precipitation in May is a critical factor on the distribution of ephemerals in Gurbantünggüt Desert.