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The embedded navigation system of autonomous underwater vehicle is introduced, which includes navigation overall architecture, hardware and software structure. The navigation system based on PC104 bus adopts the VxWorks system, which is a powerful real-time operating system. Intel PIIX-4 is used as the navigation controller's CPU. Meanwhile, the whole information flow of the navigation system is also discussed in this article. Data processes and dead-reckoning algorithm based on strong tracking Kalman filter and Singer model are presented in detail. Finally, the sea experiments which include autonomous search mission in an unknown area and long distance motion are conducted to demonstrate the reliability and feasibility of the navigation system.