Tunnels are underground structures that are widely used in geology, mining, and other related fields. Given the fact that many severe underground structure instabilities are found to be closely associated with fault systems present nearby, an integrated fault identification method, namely the 3M method, is proposed based on analyzing the macrostructure, mineral characteristics, and microstructural of rock masses in the tunnel. This method comprises three steps, and each step corresponds to one “M”: macrostructure identification, mineral analysis, and microstructure identification. First, the macrostructure is investigated to determine whether there is a fault-related feature in the tunnel, e.g., a slickenside. Second, mineral analysis infers the spatial extent of the fault from changes to the types and compositions of minerals. Third, the microstructure is investigated to determine the fault-related deformation mechanism in the tunnel, e.g., deformation twinning. Adopting the proposed method reduces the subjective influence of geological engineers and improves the accuracy of fault identification via traditional geological analysis. The results of this study provide new insight into tunnel excavation and support design.