This paper proposes a methodology to calibrate the laser scanner of a Mobile Laser Scanning System (MLS) with the trajectory of the other MLS, both of which are installed directly above the top of both rails. Railway vehicle laser scanners systems of MLS are able to obtain 3D scanning map of the rail environment. In order to adapt the actual site condition of the maintenance works, we propose a calibration method with non-linear Least Mean Square calculation which use point clouds around poles along rails and sleepers of rails as cylindrical and planner constraints. The accuracy of 0.006 m between two laser point clouds can be achieved with this method. With the common planar and cylinder condition Leven-Marquardt method has been applied for this method. This method can execute without a good initial value for the extrinsic parameter and can shorten the processing time compared with the linear type of Least Mean Square method.