The deformation in a granular soil sample subjected to shear load is localized along its directional force chain, forming an intensive failure region known as the shear zone. The particle size to the specimen size of the testing device ratio can influence the free development of the shear zone in the soil sample and its shear response. Hence, granular material's accurate macro shear response can be determined if the soil sample is free from the boundary effects induced by incorrect particle and specimen size ratio. This study utilizes the advanced 3D imaging technique to understand the localized evolution of shear bands in sand assemblies with different particle size ranges for a given specimen size of the direct shear box. The direct shear tests are conducted on three sands of different size ranges but the same size distribution: Soma sand (1.18–2 mm), rounded gravel (2–4.75 mm), and Chiba rock waste (2–4.75 mm) inside an X-ray scanning device. The scanned images at various stages of the direct shear tests are captured and pre-processed using algorithms implemented in MATLAB. The particle deformation is analysed from the X-ray tomography data in SPAM. The results provide a clear insight into microstructural evolution and indicate that when specimen size to particle size ratio is less than 6, the formation of distinct shear zone is restrained by the boundary effect and affects the macro shear response. Further, high strain zones are observed more in the case of Chiba rock than rounded gravel due to the angularity of particles.