Karst rocky desertification (KRD) is a typical fragile ecological environment with its key and difficult management point being vegetation restoration. Therefore, it is crucial to determine the adaptation mechanisms of suitable plants for ecological restoration in KRD areas. D. odorifera is a tall leguminous, woody plant with high medicinal and wood value. This study aimed to explore the adaptation strategy of the D. odorifera root system to the shallow karst fissure-soil (SKF-S) habitats. The growth, biomass, spatial root distribution, morphological characteristics, and physiological responses of D. odorifera seedlings under different treatments were studied in pots simulating SKF-S habitats. Through the experiments conducted, the following conclusions were obtained: (I) D. odorifera enhanced its ability to acquire limited resources through an allocation adjustment strategy (adjusting the biomass allocation strategy, increasing the root shoot ratio, prioritizing organ leaves and 3-level roots), which effectively offset some of the adverse effects; (II) with an increase in the stress severity, D. odorifera improved its resource acquisition adaptive strategy by reducing the root diameter and increasing the contact area with soil; (III) the spatial development characteristics of its root system were mainly manifested in the ability to grow vertically, deeper, compared to a horizontal extension; (IV) D. odorifera did not passively endure rocky desertification stress but actively improved its metabolism through root metabolic activity and SOD enzyme activity.