It is of great significance to clearly define the mineral deformation and slip system for in-depth analysis of the intrinsic mechanism of mineral response to external stress and temperature, as well as its rheological weakening process. The rapid development of science and technology and its deep integration in the geological field provide an opportunity for detailed analysis of structural deformed behavior and mechanism. This study takes quartz and amphibole in typical naturally deformed rocks as examples. Based on microstructure analysis, the comprehensive analysis was conducted on the massive mineral lattice preferred orientation data accumulated using the Electron Backscatter Diffraction (EBSD) probe mounted on the Field Emission Scanning Electron Microscope (FESEM). Based on microstructural features, EBSD mapping data, dislocation geometry types, and properties, a detailed analysis method for grain boundary trace and misorientation (axes) is elaborated. It is revealed that strain adjustment and grain refinement process of the quartz are mainly through the {m} slip system dominated by subgrain rotational recrystallization mechanism in quartz veins. It is also found that in mylonitic amphibolites, the amphibole porphyroclasts exhibit strong deformation behavior of fine-grained under the dominance of subgrain rotational recrystallization. The amphibole exhibits the interaction of multi-slip systems dominated by the [001] direction through dislocation creep in the banded amphibolites. Therefore, combining the EBSD grain boundary trace with the misorientation axis analysis method and microstructure features can completely count the micro-geological information (composition, shape, grain size, orientation, boundary, strain, etc.) of deformed minerals, and well reveal the orientation evolution law from the grain interior to between grains (or matrix). Moreover, the dominant slip system in the mineral deformation process can be effectively defined and related to the deformation environment, which has important geological significance.