Different organ morphologies determine the manner in which plants acquire resources, and the proportion of biomass of each organ is a critical driving force for organs to function in the future. Regrettably, we still lack a comprehensive understanding of root traits and seedling biomass allocation. Accordingly, we investigated and collected the seedling root morphological traits and biomass allocation of 50 annual ephemeral species to clarify the adaptation to environment. The findings of this study showed that there was a significantly negative correlation between root tissue density (RTD) and root diameter (RD) (p < 0.05), which did not conform to the hypothesis of the one-dimensional root economics spectrum (RES). On this basis, we divided 50 plant species into those rooted in dense or gravelly sand (DGS) or loose sand (LS) groups according to two soil conditions to determine the differences in root strategy and plant strategy between the two groups of plants. Our study revealed that the species rooting DGS tend to adopt a high penetration root strategy. However, the species rooting LS adopt high resource acquisition efficiency. At the whole-plant level, 50 species of ephemerals were distributed along the resource acquisition and conservation axis. Species rooting DGS tend to adopt the conservation strategy of high stem biomass fraction and low resource acquisition efficiency, while species rooting LS tend to adopt the acquisition strategy of high root and leaf biomass fraction and high resource acquisition efficiency. The research results provide a theoretical basis for the restoration and protection of vegetation in desert areas.