Characterized by depressions and elevations, the rough surfaces of faults are prone to stress concentration and energy accumulation, leading to localized rupture in the upper and lower blocks. These regions are more susceptible to stick-slip instability, manifesting various failure modes and mechanical behaviors, which are among the key factors influencing fault reactivation. Therefore, the mechanical behavior and micro-crack propagation mode of fault stick-slip under varying roughness levels necessitate further investigation. Acoustic emission monitoring is a crucial method for studying fault stick-slip failure models, enabling the acquisition of pertinent information during the fault activation process. However, the fault plane structures impede the propagation path and intensity of the rock fracture-induced acoustic emissions, thereby imposing certain limitations on examining the response mechanisms between the fault's upper and lower blocks and the rock structure surfaces. In this study, discrete-element numerical simulations were used to construct numerical models under different roughness conditions to simulate the stick-slip failure process of faults. Also, by recording the changes in mechanical behaviors among particle contacts, the acoustic emission characteristics and evolutionary patterns of fault stick-slip were investigated in more depth. The research findings show that after fault stick-slip instability motion leads to failure, microcracks are predominantly concentrated near the fault surface, with tensile failure being the primary mode. As the roughness of the fault surface increases, the failure progressively extends into the rock at the distal end of the fault. Upon slip initiation, both the total strain energy and dissipated energy exhibit a positive correlation with the roughness of the fault surface. These results provide valuable insights into the mechanical mechanisms of fault stick-slip instability motion, particularly in relation to the roughness of the fault surface.