In order to ensure that dual-axis rotational inertial navigation systems (RINSs) maintain a high level of accuracy over the long term, there is a demand for periodic calibration during their service life. Traditional calibration methods for inertial measurement units (IMUs) involve removing the IMU from the equipment, which is a laborious and time-consuming process. Reinstalling the IMU after calibration may introduce new installation errors. This paper focuses on dual-axis rotational inertial navigation systems and presents a system-level self-calibration method based on invariant errors, enabling high-precision automated calibration without the need for equipment disassembly. First, navigation parameter errors in the inertial frame are expressed as invariant errors. This allows the corresponding error models to estimate initial attitude even more rapidly and accurately in cases of extreme misalignment, eliminating the need for coarse alignment. Next, by utilizing the output of a gimbal mechanism, angular velocity constraint equations are established, and the backtracking navigation is introduced to reuse sensor data, thereby reducing the calibration time. Finally, a rotation scheme for the IMU is designed to ensure that all errors are observable. The observability of the system is analyzed based on a piecewise constant system method and singular value decomposition (SVD) observability analysis. The simulation and experimental results demonstrate that this method can effectively estimate IMU errors and installation errors related to the rotation axis within 12 min, and the estimated error is less than 4%. After using this method to compensate for the calibration error, the velocity and position accuracies of a RINS are significantly improved.