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Disturbance by rodents alters the morphologies and nutrients of plants as well as the physical-chemical properties of the soils. Changes in plants are considered to be mechanisms of defense against the disturbance by rodents. Rodents gnaw on the assimilating branches of Haloxylon ammodendron (CA Mey.) Bunge and burrow under the bushes in the desert ecosystems of Xinjiang, China. However, eco-physiological responses of different age groups of H. ammodendron to the disturbance by rodents are not well understood. In this study, soil physical-chemical properties under the shrubs and the above-ground morphological, physiological and biochemical features of assimilating branches of H. ammodendron of different age groups (i.e., young, 30?100 cm; middle-aged, 100?200 cm; and mature, >200 cm) in burrowed and non-burrowed (control) areas were studied in 2018. We found that disturbance by rodents significantly increased the crown width and total branching rates of young and middle-aged H. ammodendron. Photosynthetic pigment contents of assimilating branches of H. ammodendron were significantly reduced under the disturbance by rodents. In term of plant nutrients, the main differences among different age groups of H. ammodendron under the disturbance by rodents occurred in the total soluble sugar and reducing sugar contents that decreased in young plants, increased in middle-aged plants, and did not affect in mature plants. Crude protein and phosphorus contents significantly increased, while crude fiber and calcium contents significantly decreased in young plants. Crude fat and calcium contents significantly decreased in middle-aged plants. Soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN) and available potassium (AK) contents in the topsoil (0–20 cm), which are conducive to forming fertile islands, also increased under the disturbance by rodents. In particular, soil AN and AK were the major factors affecting the above-ground morphological characteristics of H. ammodendron in burrowed areas. Overall, the response and defense strategies of H. ammodendron to the disturbance by rodents differed among different age groups, and the effect of the disturbance by rodents on H. ammodendron gradually weakened with the increasing plant age.