During shield tunneling excavation, it is extremely important to obtain the accurate positions of the control points which determines the quality of the tunnel construction. The present process of measuring and checking the control points is labor-intensive and time-consuming. In this paper, we proposed a high-precision positioning method using a dual-axis hybrid inertial navigation system (HINS) mounted on a rail transport vehicle to measure the positions of control points automatically without other external sensors. Considering the movement constraints on the rails, an improved non-holonomic constraints (NHC) algorithm was introduced to promote navigation accuracy and a new calibration method of mounting angle errors was proposed. The semi-physics experiment and laboratory rail experiments were conducted whose results showed that the lateral position accuracy was increased by more than 94.23% and the vertical position error was reduced to the centimeter level averagely using the proposed algorithm compared to the normal INS algorithm.