To understand the role of shrubs in nebkha development, a comparative analysis of nebkha morphology and shrub features was conducted in two different habitats at the southeast margin of the Tengger Desert, Northern China. Morphometric variables of 184 Nitraria tangutorum nebkhas were measured in a semi-fixed lake-basin lowland site (site 1, n = 102) and a salinized fixed sand site (site 2, n = 82). Mean length, width, projected area, and accumulated sand volume were all greater in nebkhas in site 1 than in site 2 (p < 0.05); however, mean height (i.e., sand burial depth) did not differ significantly in nebkhas between the two sites (p > 0.05). The larger nebkha volume in site 1 relative to site 2 (mean, 88.19 m³ vs. 33.16 m³) implied that the projected area influenced the accumulated sand volume. Nebkhas in site 1 tended to have large areas, low densities, and high spatial autocorrelation, while nebkhas in site 2 exhibited opposite trends with stochastic distribution. Mean vegetation density was significantly higher in site 1 than in site 2 (p < 0.05), while mean vegetation height exhibited an opposite trend (p < 0.05). In addition, there was higher vegetation coverage in site 1 than in site 2 (p > 0.05). According to the results, plant species (i.e., N. tangutorum) limited nebkha height under similar wind regimes regardless of the transport distance of aeolian material, while aeolian deposition and its effect on shrub growth jointly increased nebkha size.