Aims Eremosparton songoricum is a rare and endangered endemic species in Central Asia. In China, it occurs in severely wind-eroded mobile and semi-mobile sand dunes of the Gurbantünggüt Desert. It has low fruit set, low seed set and rare seedling establishment. Our objectives were to determine the characteristics of populations, i.e., the variation of fruit or seed traits and seed germination among populations, to explain mechanisms of ecological adaptations of E. songoricum in different heterogeneous environments. Methods We determined the density and distance of plants and differences of shape, mass and proportion of multi-seed in six populations. Temperatures simulating those in the natural habitat of E. songoricum were used to determine the type of seed dormancy. Important findings The distance (F = 2.34, p = 0.03) and crown size (F = 8.49, p < 0.01) of plants were significantly different among populations and were highest in site C that was severely disturbed by humans. The distance and crown size located in the northeastern Gurbantunggut Desert with abundant soil moisture (E and F) were higher than populations located in the hinterland of desert (A, B, D) except population C. The characteristics of fruit and seed (length, width, thickness and mass of fruits and seeds) in the populations were significantly different but seed length and width were not. The majority of traits values were higher in populations E, F and C. The proportion of multi-seed per fruit was significantly different (F = 6.96, p < 0.01) and was highest in population C (32.50% ± 4.79%). Freshly matured E. songoricum seeds were dormant since germination percentages were <15% in all the tested temperature regimes in the populations. Scarified seeds germinated to a significantly higher percentage than non-scarified ones in all temperature regimes, indicating freshly matured E. songoricum seeds were physically dormant. A significantly lower germination percentage was recorded at 15/5 °C than at the higher-temperature regimes, indicating that low temperature inhibited seed germination. Large-seeded populations (C, E and F) had higher germination percentages (<70%) than small-seeded populations (A, B and D; <50%) after scarified treatments (F = 30.77, p < 0.01), indicating that seeds from all populations had physical and physiology dormancy (PY + PD). The varying degree of PY + PD of E. songoricum seeds in different populations may be an important survival strategy for E. songoricum in the heterogeneous environments in the Gurbantünggüt Desert.