To enhance the service performance of the subgrade and optimize subgrade design, we conduct a comprehensive analysis of the impact of gradation on the mechanical properties of crushed stone aggregates, considering both macroscopic and microscopic perspectives. And this paper establishes intricate relationships between deformation parameters, fragmentation, and gradation within crushed stone aggregates, shedding light on the nuanced variations in microscopic mechanical properties across various gradations. The research outcomes underscore that the cumulative deformation and resilience modulus of crushed stone aggregate gradually stabilized after 1000 loadings. The curvature coefficients of gradations 3 and 4 were significantly smaller than those of gradations 1 and 2, which were 1.09 and 0.92, respectively. The gradations with smaller curvature coefficients had better uniformity and density. The addition of limestone increased the resilience modulus of aggregate, but also increased the cumulative deformation. The best effect was achieved when the ratio of quartz to limestone in the aggregate was 3:1. For the failure form of crushed stone aggregate, the failure form of gradation 1 with less fine particle content was mainly characterized by crushing, while the failure forms of gradations 2, 3, and 4 were mainly grinding. When limestone was added to the aggregate, the failure form was also mainly grinding. In addition, the crushing degree of crushed stone aggregate was closely related to the change in the distribution coefficient r. The smaller the change, the lower the crushing degree. The crushing degree was the smallest when gradation 4 and the ratio of quartz to limestone was 3:1, and the change values were 0.038 and 0.073, respectively. The simulation results further show that when the aggregate gradation is 4 or the limestone content is less than 50%, the microcrack content decreases, while the microcracks and force chains are more uniformly distributed.