Nitraria tangutorum nebkhas play a vital role in maintaining ecosystem stability in arid desert environments, yet the coupled relationships among their morphology, biomass allocation, and soil seed bank diversity remain poorly understood. In this study, we investigated N. tangutorum nebkhas in the Ulan Buh Desert to explore how shrub canopy cover and nebkha volume jointly influence morphological characteristics, biomass distribution, and soil seed bank diversity. N. tangutorum nebkhas were classified into three canopy cover levels (high, medium, and low) and three volume classes (large, medium, and small). We established quantitative relationship models among morphological parameters, biomass components, and their interactions to clarify the structural linkages and their ecological implications. Morphological and biomass traits explained 67%, 58%, 55%, and 74% of the variation in the Shannon, Simpson, Chao1, and Pielou indices of the soil seed bank, respectively. Based on canopy cover and volume, three developmental stages were identified: formation, stabilization, and degradation. During these stages, biomass allocation shifted from being shoot-dominated to root-dominated, and finally to an approximate balance between the two. Using generalized additive models, we determined the threshold responses of soil seed bank diversity to morphological and biomass changes and discussed the underlying mechanisms. Our findings provide new insights into the coupling among morphology, biomass, and soil seed bank diversity in desert shrub nebkha systems and enhance the understanding of vegetation-geomorphology interactions in arid ecosystems.