In high-precision navigation applications, a well-designed self-calibration method is a convenient approach to ensuring the positioning performance of a rotational inertial navigation system (RINS). Benefiting from the gimbal structure, traditional inertial measurement unit (IMU) sensor errors, including gyro drifts, accelerometer biases, scale factor errors and installation errors, could be estimated through a filter process under a proper rotation scheme. However, when the IMU rotates, inner lever-arm effects may bring additional errors to the observations, which may reduce the self-calibration accuracy. In this paper, an improved self-calibration method that includes consideration of the inner lever-arm effect is proposed for a dual-axis RINS. Based on analysis of the error propagation characteristics, a novel rotation scheme with variable angular rate is designed. By adopting the proposed self-calibration method, traditional IMU sensor errors can achieve much higher accuracy, and the inner lever-arm parameters can also be well calibrated simultaneously. Long-term vehicle navigation indicates that the positioning accuracy was significantly enhanced after the compensation of the calibration results, fully illustrating the effectiveness of the proposed method in ameliorating navigation performance for the dual-axis RINS.