During the operation of sandy railways, the challenge posed by wind-blown sand is a persistent issue. An in-depth study on the influence of wind-blown sand content on the macroscopic and microscopic mechanical properties of the ballast bed is of great significance for understanding the potential problems of sandy railways and proposing reasonable and adequate maintenance and repair strategies. Building upon existing research, this study proposes a new assessment indicator for sand content. Utilizing the discrete element method (DEM) and fully considering the complex interactions between ballast and sand particles, three-dimensional (3D) multi-scale analysis models of sandy ballast beds with different wind-blown sand contents are established and validated through field experiments. The effects of varying wind-blown sand content on the microscopic contact distribution and macroscopic mechanical behavior (such as resistance and support stiffness) of ballast beds are carefully analyzed. The results show that with the increase in sand content, the average contact force and coordination number between ballast particles gradually decrease, and the disparity in contact forces between different layers of the ballast bed diminishes. The longitudinal and lateral resistance of the ballast bed initially decreases and then increases, with a critical point at 10% sand content. At 15% sand content, the lateral resistance is mainly shared by the ballast shoulder. The longitudinal resistance sharing ratio is always the largest on the sleeper side, followed by that at the sleeper bottom, and the smallest on the ballast shoulder. When the sand content exceeds 10%, the contribution of sand particles to stiffness significantly increases, leading to an accelerated growth rate of the overall support stiffness of the ballast bed, which is highly detrimental to the long-term service performance of the ballast bed. In conclusion, it is recommended that maintenance and repair operations should be promptly conducted when the sand content of the ballast bed reaches or exceeds 10%.