Studying the frictional process, acoustic emission (AE) characteristics and permeability evolution of fractures under water injection is fundamental for proposing theories and methods to control the stability of geological structures. In this work, the shear-flow test was conducted on Longmaxi shale fractures with different specific roughness to analyze the frictional deformation and mechanical properties of shale fractures during the frictional slip process, and the influence of effective normal stress and surface morphology was investigated. AE monitoring technology was also utilized to reveal the AE evolution during the frictional slip process. Based on the AF/RA values, AE signals were subjected to cluster analysis using the Gaussian Mixture Model (GMM) to distinguish and quantify the crack types and proportions during frictional slip. Combining the development of cracks and considering the ratio of worn area, a theoretical analytical expression was established to reasonably describe the friction-damage evolution, classifying the friction-damage during the frictional slip process into tensile and shear damage, respectively. Meanwhile, the permeability evolution of Longmaxi shale fractures was also studied in detail. A theoretical model capable of describing and predicting the permeability evolution was proposed under the condition that the permeability evolution and damage process of Longmaxi shale fractures correspond to each other. Finally, the interaction between asperities on shale fractures with different surface morphologies during the frictional slip process was discussed, and the influence mechanism of surface morphology on permeability evolution was revealed.