Kaxiutata iron deposit is a skarn type magnetite deposit located in Inner Mongolia, China. There are many faults developed after metallogenic period. In this study, NIR analysis method is adopted to identify the mineral composition of subsurface and surface fault gouge from mining area. Through the characteristic peaks, it is was identified that there are mainly mafic mineral in the subsurface fault gouge and salic minerals in the surface fault gouge, the sand sample for comparison contain both two types of minerals. The result of analysis of all three sets of sample is in accordance with the geological background of the sampling spot. According to this research, due to the main composition of the fault gouge in the mineralization area are clay formed due to the faulting movement and altered minerals formed in early metallogenic period. NIR analysis technology is suitable for this type of sample, to use this technology, we can identify the clay mineral in the fault gouge, and further speculate the composition of protolith of clay, we can also indentify the altered minerals formed in metallogenic period, and provide useful information for study of hydrothermal deposit.