Since a conventional petrographic analysis does not allow a systematic and detailed study on how the microscopic factors affect the macroscopic behavior of inter-layered rocks, this research adopted a numerical model, the bonded particle model, to explore the micro-mechanisms associated with the strength and stiffness of inter-layered rocks. The model was first calibrated by comparing the simulations to the actual behavior until they tally with each other. Following, the microscopic factors, including the bond strength, the bond stiffness, type of bonds and friction of particles and type of bond stiffness, are varied to study their influences. As expected, the bond strength and the bond stiffness are found to have a direct and significant influence on the macroscopic uniaxial compressive strength and stiffness, respectively. Furthermore, close observations on the breaking of bonds during the loading process reveal interesting phenomena, including the transition of shear/normal bond breaking, the type of internal fracture and the factors controlling internal failure, etc. These phenomena enlighten the interpretations about the micromechanisms accounting for the macroscopic strength and stiffness of inter-layered rocks.