To estimate the location of the train, we consider an integrated navigation system that combines Inertial Navigation System (INS) and Global Navigation Satellite System (GNSS). This system provides accurate navigation results in open sky by combining only the advantages of both systems. However, since measurement update cannot be performed in GNSS signal blocked areas such as tunnels, mountain, and urban areas, pure INS is used. The error of navigation information increases in this area. In order to reduce this problem, the train's Non-Holonomic Constraints (NHC) information can be used. Therefore, we deal with the INS/GNSS/NHC integrated navigation system in this paper. However, in the process of installing the navigation system on the train, a Mounting Misalignment Error of the IMU (MMEI) inevitably occurs. In this case, if the NHC is used without correcting the error, the navigation error becomes even larger. To solve this problem, a method of easily estimating the MMEI without an external device is introduced. The navigation filter is designed using the Extended Kalman Filter (EKF) by considering the MMEI. It is assumed that there is no vertical misalignment error, so only the horizontal misalignment error is considered. The performance of the integrated navigation system according to the presence or absence of the MMEI and the estimation performance of the MMEI according to the method of using NHC information are analyzed based on simulation. As a result, it is confirmed that the MMEI is accurately estimated by using the NHC information together with the GNSS information, and the performance and reliability of the integrated navigation system are improved.