Landscape fragmentation, a widespread phenomenon, is considered a process by which the landscape not only breaks up and disjoints, but also changes from simple to complex status owing to disturbance by anthropogenic or other factors. Eremurus inderiensis (Liliaceae) is a perennial ephemeral geophyte herb. In China, E. inderiensis grows on fixed and semi-fixed sand dunes of the Gurbantunggut Desert in the Xinjiang Uyghur Autonomous Region. This kind of ephemeral plant contributes greatly to the stabilization of sand. Nowadays, increasing human activities have fragmented the original habitats of E. inderiensis populations in the southern Gurbantunggut Desert, resulting in numerous separate population patches. The sizes of plant populations in different patchy habitats directly reflect plant response characteristics and adaptation strategies to the environment. The study of plant flowering and fruiting characteristics and seed morphology and germination characteristics will help to understand plant survival strategy and evolutionary trends in different habitats. In this paper, we used E. inderiensis as the research object. Based on field investigation, we studied the population size and reproductive traits of this plant to reveal ecological adaptability of E. inderiensis in different patchy populations. Our results showed that there were significant differences in the population size and seedling proportion in different patches. Less fragmented patches had larger population sizes; the proportion of seedlings high in large populations and low in small populations. Small populations had lower flower number, fruit number, seed number, natural fruiting rate, and seed setting rate, with significant differences among populations. With the increase of habitat fragmentation, 1000-seed weight, seed length, and seed width showed a decreasing trend, while the proportion of seed wing showed an increasing trend. Seeds began to germinate after 20-30 days. The patch populations with different fragmentation degrees had different germination trends, and the maximum germination rate was achieved in about 40-50 days. Seed germination rate showed a decreasing trend with increasing habitat fragmentation. Further studies are needed to examine the effects of different combinations of disturbance factors on E. Inderiensis population status in different habitats to formulate scientific and practical protection and recovery strategies for this plant.