Rodents, such as those that feed on plants and nest in plant roots, can significantly affect the growth and development of desert plants. The aim of this study was to investigate the effects of Rhombomys opimus disturbance on the photosynthetic characteristics and nutrient status of Haloxylon ammodendron at different growth stages in the Gurbantunggut Desert. The effects of great gerbil disturbance on the photosynthetic characteristics of H. ammodendron at different growth stages were investigated by measuring the gas exchange parameters, instantaneous water use efficiency, and chlorophyll fluorescence parameters of H. ammodendron at different ages (young, middle, and adult) under the disturbance of great gerbils. The soil nutrients in the assimilated branches and rhizosphere of H. ammodendron at different growth stages were tracked to reveal the relationship between the H. ammodendron nutrient content and gerbil disturbance. The results showed that great gerbil disturbance decreased the organic carbon content in the rhizosphere soil of adult H. ammodendron and increased the total nitrogen content in the rhizosphere soil and the nitrogen and potassium contents in the assimilated branches at each growth stage. The net photosynthetic rate and instantaneous water use efficiency of H. ammodendron decreased at each growth stage, and the maximum photochemical efficiency and non-photochemical quenching parameters of the young H. ammodendron decreased. However, the actual photochemical efficiency and photochemical parameters of the middle H. ammodendron increased. It was concluded that the disturbance of great gerbils decreased the photosynthetic capacity of H. ammodendron and increased the content of total nitrogen in the soil and nitrogen and potassium in the plant. This study revealed that the Gurbantunggut Desert great gerbil and H. ammodendron do not have a simple predation relationship. It laid a foundation for the study of the moderate disturbance threshold and better use of the mutually beneficial relationship between the two.