We propose a 3D-shape preferred orientation (SPO) measurement method of rigid grains using synchrotron micro-computational tomography (μ-CT). The method includes oriented sampling, 3D μ-CT imaging, image filtering, ellipsoid fitting, and SPO measurement. After CT imaging, all processes are computerized, and the directions of thousands of rigid grains in 3D-space can be automatically measured. This method is optimized for estimating the orientation of the silt-sized rigid grains in fault gouge, which indicates P-shear direction in a fault system. This allows us to successfully deduce fault motion sense and quantify fault movement. Because this method requires a small amount of sample, it can be applied as an alternative to study fault systems, where the shear sense indicators are not distinct in the outcrop and the fault gouge is poorly developed. We applied the newly developed 3D-SPO method for a fault system in the Yangsan fault, one of the major faults in the southeastern Korean Peninsula, and observed the P-shear direction successfully