The scale effect in rockfill materials leads to distinct differences in mechanical characteristics between scaled and prototype particles, primarily due to the inherent size dependence of particle crushing strength (PCS). This study presents a factorial design to clarify how microstructural heterogeneity and contact conditions govern the size effect of PCS. Discrete element simulations, validated against experimental results for limestone particles ranging from 20 to 60 mm through comparisons of force–displacement responses, Weibull statistics, and power-law size-strength relationships, are adopted to assess the relative importance of controlling factors. Based on 1920 single particle crushing simulations, elastic modulus is identified as the dominant factor affecting the size‑effect coefficient, followed by internal porosity. Joint effects between (i) elastic modulus and particle morphology, and (ii) the size ratio of elementary balls and particle morphology, also contribute non-negligibly to variations in PCS size dependence. Further analysis of the underlying mechanisms shows that particles with higher elastic modulus develop smaller contact areas and stronger internal stress concentrations, which in turn increase the variability of PCS and intensify the size effect. In contrast, for larger particles, compact pore clusters act as critical internal flaws and therefore lead to a more pronounced size effect with increasing internal porosity. These findings provide new insights into the governing factors of the size effect of PCS and may contribute to the development of more comprehensive constitutive models for crushable materials.