Terrain Elevation Matching(TEM) uses terrain height variations under an aircraft and the reference map stored on-board to get the aircraft position.Hidden-Markov-Model(HMM) was applied to construct a new TEM model,viz.HMM based TEM (HMMTEM) model.With the given model,an HMMTEM algorithm using Viterbi,is designed and implemented to estimate the position error in INS.The simulation results show that HMMTEM algorithm can better improve the positioning precision of autonomous navigation than SITAN algorithm.