The scale effect is considered one of the most significant factors governing the mechanical behavior of rocks. This study investigated the influence of the height-to-diameter ratio (H/D) and grain arrangement on the uniaxial compressive strength (UCS) and modulus of elasticity (E) of granite using finite element modeling. For this purpose, samples with three grain arrangements including irregular, medium regular, and almost regular were generated and simulated under uniaxial compression for H/D ratios of 0.8, 1.4, and 2. The results indicated that increasing the H/D ratio from 0.8 to 2 led to a reduction in average UCS values ranging from 17% to 26% across all grain structures. In contrast, the modulus of elasticity exhibited lower sensitivity to changes in sample dimensions, with a reduction ranging between 4% and 8%. The analysis of grain arrangement effects showed that disordered structures, with greater scatter in UCS values, exhibit the highest sensitivity to the scale effect, whereas more regular networks, due to a more uniform stress distribution, produce more mechanically stable behavior. To quantitatively analyze the scale effect, power relationships were derived between the mechanical parameters and the H/D ratio. The analyses indicated that the scale effect sensitivity coefficient for UCS is significantly higher than that for the modulus of elasticity; specifically, the ratio of the scale effect intensity of UCS to E ( ) in medium regular structures was estimated to be 4.9. This study showed that scale effect of granite is mainly resistive and strongly controlled by microstructural heterogeneity and grain arrangement.