Accurate assessment of anisotropy and scale effect of rock joint roughness is essential for evaluating the mechanical behaviour of rock joints. However, in previous studies, how to quantify roughness anisotropy of rock joints remains largely unsolved, and the research about scale effect on roughness anisotropy is not conclusive. A statistical analysis on joint roughness coefficient of different sized profiles was implemented to investigate the scale-dependency of joint roughness. The scale effect on the roughness anisotropy were investigated based on class ratio transform approach. The roughness anisotropy was characterized by local anisotropy and global anisotropy. The global anisotropy tends to be almost constant when the sample size exceeds the stationarity threshold length of 70 cm. The result shows that the global anisotropy is scale-dependent. However, the scale effect on local anisotropy is less apparent. The case study indicates that the class ratio transform approach implies its superiority in roughness anisotropy investigation.