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Inertial orientation systems have many potential uses beyond air- and spacecraft applications. Compared to the conventional large-scale system, the novel aspects of an orientation system based on micro electromechanical systems (MEMS) are small size, lightweight, low-power consumption, and low cost by the inclusion of microsensors with on-chip functionality, such as micromachined rate gyroscopes, accelerometers, and etc. However, the performance associated with these low-cost MEMS sensors is generally not satisfied. A conventional strapdown method based on integral of angular rate to figure out attitudes will inevitably induce long-term drift. For eliminating this accumulative error and thus using the low-cost navigation system for a long-duration mission, a hybrid configuration by combining a MEMS-based azimuth-level detector with the conventional strapdown system is proposed in this paper. The azimuth-level detector is composed of three-axis MEMS accelerometers and three-axis MEMS magnetometers. With an absolute solution based on the gravity and the earth magnetic field rather than the integral algorithm, attitude and heading estimation without drift errors can be obtained so as to facilitate adjusting the attitude and heading for the conventional strapdown system. The hierarchical computation process for estimating the attitude and heading using the hybrid system is depicted first. Then, comprehensive system errors including transformation errors of the computation, such as skew, scale, and drift errors, are analyzed. Finally, it is verified by both of formula analysis and experimental test that the accumulative errors can be effectively eliminated via this hybrid scheme.