[Objectives] The relationship between food resources and animal population size has long been a focal point in ecological research. Regarding mechanisms of the effects of food resources on animal populations, the hypotheses of food quality, plant secondary metabolites, and food quantity have been proposed. The effect of related mechanisms on the seasonal scale is not clear. Therefore, this study investigates the relationship between seasonal variations in food resources and the population density of the Three-Toed Jerboa (Dipus sagitta) in the Alxa desert area. [Methods] From 2018 to 2022, 12 sampling areas were randomly selected in the Alxa desert, and a 5 hm² quadrat was randomly set up in spring, summer, and autumn. The number of Three-Toed Jerboas was investigated by the trap-day method, and their feeding habits were determined. At the same time, the plant community survey was carried out in the quadrat. The mixed linear model was adopted to compare the seasonal differences in the population density of female and male Three-Toed Jerboas (α = 0.05). The plant biomass, food biomass, preferred plant biomass, and unused plant biomass based on plant quadrats and the diet data of Three-Toed Jerboas were calculated (Fig. 1). Factor analysis was conducted to examine the relationship between each variable and the population density of male and female Three-Toed Jerboas (KMO > 0.5, Bartlett sphericity test P < 0.05). The contribution of each variable to the factor was determined by the factor loading coefficient, which is the correlation coefficient between the original variable and the common factor. [Results] The population density of female and male Three-Toed Jerboas was significantly different between seasons (Fig. 2). Male and female Three-Toed Jerboas fed on different plants during the seasons and were selective about plants in their habitats (Fig. 3). In spring, the population density of male and female Three-Toed Jerboas was positively correlated with annual herbaceous biomass and food biomass (Appendix 2, Table 2). The population density of male Three-Toed Jerboa was positively correlated with its preferred shrub biomass and annual herbaceous biomass (Table 3). In summer, the population density of male and female Three-Toed Jerboas was positively correlated with shrub food biomass (Table 2) and preferred shrub biomass (Table 3). In autumn, the population density of male and female Three-Toed Jerboas was negatively correlated with perennial herbaceous biomass (Appendix 2) and positively correlated with shrub food biomass (Table 2). The population density of female Three-Toed Jerboas was positively correlated with preferred shrub biomass (Table 3). [Conclusion] Seasonal fluctuations of food resources co-vary with the seasonal changes in plant selection by Three-Toed Jerboas in their habitats. The population density of male and female Three-Toed Jerboas is influenced by food availability in their habitats, with noticeable seasonal effects. Therefore, this study supports the food resource hypothesis for animal population fluctuations.