Persistency, as a key geometric parameter of joints, significantly affects shear strength parameters of jointed rock mass. A good understanding of how persistency affects shear behavior of joint is therefore crucial for better evaluation of stability of rock slope. To investigate the failure and micro-cracking behavior of non-persistent rock joint under direct shear, a novel Voronoi generation algorithm is first used to establish an improved grain-based model (GBM) of granite which considers the shape of feldspar. The calibrated model is then used to simulate the direct shear test of numerical models possessing different joint persistency under various normal stresses. The results reveal that the developed micro-cracks generally increase rapidly when the shear strain reaches to a value approximately 50 % of the peak shear strain and the grain boundary tensile micro-crack is dominant among these initiated micro-cracks. Micro-cracks generally initiate at the ends of rock bridge, and then gradually propagate to the central of rock bridge, forming en-echelon fractures. The failure mode of numerical model is closely related to the generated en-echelon fractures. An increase in both joint persistency and normal stress can lead to a shear failure. The finding in this study provides an important basis for understanding the mechanical behavior and failure mechanism of jointed rock mass.