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Underwater robotic navigation system is one of challenge issues of autonomous underwater robotics, and it is also the underwater robotics' difficult field and active research field. An inertial integrated navigation system, which is based upon inertial measurement unit, Doppler velocity log, TCM2, GPS and ultra-short base line, is designed for underwater robotics in this paper. The configuration and measurement sensors of the navigation system are analyzed, and an estimation algorithm based on multi-layer Kalman filtering is presented in particular. Furthermore, in order to deal with the position information delay of sensors, dead-reckoning estimation algorithm and double-layer estimation algorithm are proposed. Simulation results validate the correctness and usability of the integrated navigation system and the validity of these algorithms.