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Mobile laser scanning (MLS) point cloud registration plays a critical role in mobile 3D mapping and inspection, but conventional point cloud registration methods for terrain LiDAR scanning (TLS) are not suitable for MLS. To cope with this challenge, we use inertial measurement unit (IMU) to assist registration and propose an MLS point cloud registration method based on an inertial trajectory error model. First, we propose an error model of inertial trajectory over a short time period to construct the constraints between trajectory points at different times. On this basis, a relationship between the point cloud registration error and the inertial trajectory error is established, then trajectory error parameters are estimated by minimizing the point cloud registration error using the least squares optimization. Finally, a reliable and concise inertial-assisted MLS registration algorithm is realized. We carried out experiments in three different scenarios: indoor, outdoor and integrated indoor–outdoor. We evaluated the overall performance, accuracy and efficiency of the proposed method. Compared with the ICP method, the accuracy and speed of the proposed method were improved by 2 and 2.8 times, respectively, which verified the effectiveness and reliability of the proposed method. Furthermore, experimental results show the significance of our method in constructing a reliable and scalable mobile 3D mapping system suitable for complex scenes.