The deformation process and failure mechanism of rock mass with increased density of initial joints subjected to confined stress state are investigated in this study using discrete element method (DEM). A numerical model of standard size granite samples is developed and validated using experimental data for both intact and jointed rocks. The micro-parameters of the rock material are first determined, and the effects of the rock discontinuity on strength, deformability, stress–strain relationship, and failure modes are then investigated at the macro-scale level. Analyses are also performed to examine the tensile and shear crack distributions, fragmentation characteristics, particle kinematics, and energy dissipation to advance the current understanding of the deformation processes and failure mechanisms of jointed rock masses. The microscopic evolutions in the fabric and force anisotropy during loading and distributions of contact forces provide insights into the influence of increasing initial jointing on the macroscopic deformational behavior of the rock. The results show how the deceleration in the growth of fabric and contact force anisotropies develops and confirms that the increase in initial jointing and the associated changes in microstructure can restrain the development of anisotropy, thereby reducing significantly the strength of the rock samples.