Discontinuities mainly control the mechanical behavior of rock mass and cause a significant reduction in the rock mass strength. Joint persistency and joint infill conditions are considered the most significant joint parameters that control the mechanical response of rock mass. In this study, numerical and statistical analyses were performed on pre-cracked specimens with two flaws to investigate the effect of joint persistence parameters on shear strength. In addition, an extensive study was conducted to explore the effect of infilled mineral strength, infill thickness, and infill wall roughness on shear strength. The Lattice-Spring-Based Synthetic Rock Mass (LS-SRM) approach was utilized to perform the numerical models. The results showed that the tensile crack propagation is limited at higher normal stresses as tensile damage is largely suppressed. The increases in rock bridge angle slightly increased the shear strength and caused a change in the failure mechanisms of the rock bridge from tensile to shearing. The results of the models with infilled minerals revealed that infilled minerals mainly controlled the shear strength of specimens when the infill thickness was 4.0 mm or greater. The infill wall roughness had no apparent effect on the shear strength. In contrast, it governed the failure mechanisms; cracks initiated at the asperity of the rough filling wall and propagated through the hosted rock mass.