Research on the temporal and spatial dynamics of non-structural carbohydrates (NSC) in plants and their distribution patterns in different modules will help understand the effects of environmental changes on plant growth and the ecological adaptation strategies of plants to heterogeneous environments. In this paper, Phragmites australis L., as a typical clonal plant in inland river wetlands, was analyzed to determine the characteristics of the variation in NSC and their compositions (soluble sugars: SS and starch: S) in early growth, mid-growth and later growth seasons at three habitats (wet, salt marsh, drought). The results showed that (1) the contents of NSC, SS and S in the whole plant and clonal modules of P. australis showed seasonal variations with gradually increasing trends in wet, salt marsh and drought habitats, but the SS contents of leaves displayed seasonal variations with decreasing trends; (2) there were differences in NSC's allocation strategies across clonal modules, showing that the NSC and SS were mainly invested in rhizomes and were transferred from leaves to stems, while S were mainly invested in stems and was transferred from rhizomes to roots during the transition from wet to drought habitat. The growth and survival strategies of clonal plants in inland river wetlands are dependent on the accumulation and allocation of NSC and their compositions. Meanwhile, these were the great significance guiding for the protection of inland river wetlands in the arid area.