Deformation monitoring is beneficial to ensure the service safety of long tunnel. An three-direction (vertical, transverse and axial) deformation estimation method using long-gauge fiber Bragg grating (FBG) sensing technology is proposed and applied to a long tunnel by integrating mechanical analysis and field monitoring during the service state. The key issues of the proposed method for identifying the three-direction deformation are discussed, such as establishing the separation model of coupling strain on cross section, deriving the theory of deformation identification in three directions, and determining the sensor layout of the long tunnel. A major advantage of the proposed method is that the three-direction deformation of the tunnel can be monitored in real time using distributed long-gauge strain sensors. The numerical analysis and field test results verify the feasibility of the proposed method.