In desert regions, the service life of railways is threatened by wind-blown sand. To investigate the impact of wind-blown sand penetration on the micromechanical behavior and energy evolution of ballast particles, this paper conducted field dynamic testing of the track structure and proposed a new sediment concentration index calculation method. Using the "layered generation-stepwise filling" approach, a series of three-dimensional, multi-scale, high-fidelity discrete element analysis models of sandy ballast beds with different sediment concentrations were developed. The results show that at 33 % sediment concentration, the wheel-rail vertical force and dynamic bending stress of the rail rise by 19.97 % and 11.59 %, respectively, compared to those at 0 % rail, 3.89 g on the sleeper, and 0.76 g in the ballast bed, changing by 9.21 %, 22.33 %, and -47.22 %. The translational and rotational kinetic energy of ballast particles both first increase then decrease as sand rises, with 12 % as a critical inflection. This reflects the critical transition between the lubrication effect at the low sediment concentration and the interlocking effect at the high sediment concentration, which warrants particular attention. The potential energy of ballast particles is positively correlated with sediment concentration. When the sediment concentration increases to 33 %, potential energy increases to 996.786 J, representing an 11.37 % increase compared to the 0 % sediment concentration. These results reveal the evolutionary mechanism of sand particle filling, interlocking, and hardening, providing theoretical support for optimizing maintenance strategies for wind-blown sandy railways.