Autonomous navigation microsystem is one of the core technological directions for the development of terminal user navigation systems toward miniaturization, integration, and intelligence under the new generation national comprehensive positioning, navigation and timing architecture. They hold significant application value in fields such as deep space exploration, microsatellites, and autonomous operation of space vehicles. To address the issues of non-stationary drift and multi-mode failures in autonomous navigation microsystems under complex space environments, this paper proposes a systematic solution based on synergistic enhancement of hardware hardening and software intelligence, which comprehensively improves their accuracy retention capability and environmental adaptability of autonomous navigation microsystems in complex space environments from three levels: microstructure, algorithm, and system integration. At the hardware level, radiation-hardened micro-inertial sensor structures and low-noise application-specific integrated circuits are designed and implemented to improve intrinsic robustness under coupled mechanical, thermal vacuum, and radiation environments at the physical source. At the software level, a device-level compensation method based on piecewise polynomial fitting across the full temperature range is proposed. By employing adaptive temperature zone partitioning and an online parameter fine-tuning mechanism, real-time dynamic compensation of relevant errors is achieved. Based on this approach, a low-power, high-reliability engineering prototype is designed and developed, and comprehensive space environmental tests, including temperature cycling, vibration and shock, and total dose irradiation, are conducted. The experimental results demonstrate that the developed autonomous navigation microsystem achieves an angular rate bias stability of better than 2°/h(1 σ,10 s) and an acceleration bias stability of better than 100 μg(1 σ,10 s). The bias output variation before and after vibration for each angular rate measurement axis is less than 50°/h, and for each acceleration measurement axis, it is less than 6mg. Under a total dose test of 40 krad(Si), the bias variation before and after irradiation is less than 16%. This research provides support for long-life and highreliability autonomous navigation of micro aerospace vehicles.