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Plant organ biomass allocation and morphological characteristics are important functional traits. The responses of plant root, stem, and leaf traits to heterogeneous habitats in floodplain wetlands are highly important for understanding the ecological adaptation strategies of riparian plants. However, the patterns of these responses remain unclear. In a floodplain wetland in the middle reaches of the Heihe River, we studied the responses of the root, stem, and leaf morphological traits and biomass allocation of Leymus secalinus to varying habitat conditions. We measured these traits in three sample plots, delineated based on distance from the riverbank: plot I (near the riparian zone, 50–150 m from the riverbank), plot II (middle riparian zone, 200–300 m from the riverbank), and plot III (far riparian zone, 350–450 m from the riverbank). The results showed that in plot I, L. secalinus tended to have slender roots and stems and small leaves, with a biomass allocation strategy that maximized the root–shoot ratio (RSR). In plot II, L. secalinus had thick stems and moderate leaf and root patterns, and the RSR values were between those of plot I and plot III. In plot III, L. secalinus had thin and short stems and large leaves; furthermore, among the root morphological structures, plot III had the shortest Rhizome length (RL) and longest Rhizome diameter (RD), and the RSR was the lowest. Moreover, there was a significant correlation between organ biomass and leaf thickness, stem length, RD, and RL in the three habitats (p < 0.05). By balancing the biomass allocation among organs, wetland plants in floodplains balance changes in root, stem, and leaf morphological characteristics to improve their environmental adaptation.