Recently, X-ray micro-tomography has been utilized for characterization of deformation and fracture behaviors in materials. The micro-tomography that is available in the synchrotron facility can reveal the existence of particles and crack in about 1 μm resolution. In this study, three-dimensional mapping technique has been developed to observe inhomogeneous plastic deformation affected by metallurgical microstructures in small specimen. Marker-tracking method with predicting marker position was produced to obtain strain in inhomogeneously and highly deformed region. The model that simulates tensile test was produced with taking actual deformation pattern into consideration. Evaluation of ratios of success tracking and tracked marker showed good performance of the developed method. The prediction of marker position after deformation was very effective in tensile deformation with necking. Almost 100% ratios of success tracking and tracked marker were indicated not only in homogeneous deformation up to 10% strain but also in inhomogeneous deformation up to 5% strain.