Filling materials in fracture significantly affect the mechanical behaviors of single rough rock fractures, but the difference of natural open and infilled fracture during shear has not been entirely understood and requires further investigation. In this study, direct shear tests were performed on the Beishan natural open and infilled granite fractures, respectively. The evolution of asperity damage during shear was monitored using acoustic emission (AE) technique, and the asperity degradation zones and damage volumes caused by shear were evaluated with the 3D blue light scanner. A laser diffraction particle size analyser was used to examine the size distribution of sheared-off fragments. The results showed that the shear strength of infilled granite fractures is larger than that of natural open fractures under a lower normal stress because of the cohesive strength, which is different from most artificial fractures with unconsolidated infilled materials. With the increase of the normal stress, the shear strength of open fracture may exceed that of infilled fracture. The size of the sheared-off fragments in both kinds of fractures under different normal stresses was found to follow a Weibull distribution but particle size tended to be smaller in infilled fracture. Combining the proposed joint damage coefficient and the Weibull size distribution of the sheared-off fragments can approximately predict the potential effects of sheared-off fragments on solute retardation coefficient for infilled fractures. The acoustic emission ringing count and accumulated AE energy of two kinds of fractures follow the same law but tend to be more drastic in open fracture, which complain the two main modes of asperity degradation during shear, i.e., instantaneous failure of asperities occurring at the peak shear stress, and crushing of the generated fragments with further shear displacement.