The use of terrestrial laser scanning (TLS) point clouds for tunnel deformation measurement has elicited much interest. However, general methods of point-cloud processing in tunnels are still under investigation, given the high accuracy and efficiency requirements in this area. This study discusses a systematic method of analyzing tunnel deformation. Point clouds from different stations need to be registered rapidly and with high accuracy before point-cloud processing. An orientation method of TLS in tunnels that uses a positioning base made in the laboratory is proposed for fast point-cloud registration. The calibration methods of the positioning base are demonstrated herein. In addition, an improved moving least-squares method is proposed as a way to reconstruct the centerline of a tunnel from unorganized point clouds. Then, the normal planes of the centerline are calculated and are used to serve as the reference plane for point-cloud projection. The convergence of the tunnel cross-section is analyzed, based on each point cloud slice, to determine the safety status of the tunnel. Furthermore, the results of the deformation analysis of a particular shield tunnel site are briefly discussed.