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Eremosparton songoricum (Litv.) Vass. experiences different soil water availabilities under wild conditions, suggesting that variation in soil water is ecologically relevant for this species. The reproductive traits of E. songoricum were estimated in response to drought and were compared in two populations with highly heterogeneous water resources in the Gurbantunggut Desert: Population A at the riverside desert with better water condition and Population B at the hinterland desert with worse water condition. Results showed that the duration of flowering lasted for 25 d and 21 d for population A and B respectively from late May to late June. In population B, the anthesis of a single flower, flowering branch number per plant, inflorescence number per flowering branch, flower number per inflorescence, and seed mass of a hundred seeds were significantly lower, however, the nectar secretion per flower, visitation rate by effective pollinators, duration of visit on each flower, and fruit set were significantly higher than in population A. Seed set didn’t respond to drought. Results showed that E. songoricum produced smaller floral display sizes in population B which might save more resources for nectar production, thereby eliciting long duration on flowers and more fruit set, which are the adaptative strategies to droughty habitat. Mass of hundred seeds was smaller in population B, which is an advantage in extending the dispersal distance under favorable habitat because of the decreased weight of the dispersal fruit. Thus the smaller floral sizes will be advantageous in maintaining reproductive success under drought habitats for E. songuricum.