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At present, simultaneous localization and mapping (SLAM) for an autonomous underwater vehicle (AUV) is a research hotspot. Aiming at the problem of non-linear model and non-Gaussian noise in AUV motion, an improved method of variance reduction fast simultaneous localization and mapping (FastSLAM) with simulated annealing is proposed to solve the problems of particle degradation, particle depletion and particle loss in traditional FastSLAM, which lead to the reduction of AUV location estimation accuracy. The adaptive exponential fading factor is generated by the anneal function of simulated annealing al-gorithm to improve the effective particle number and replace resampling. By increasing the weight of small particles and decreasing the weight of large particles, the variance of particle weight can be reduced, the number of effective particles can be increased, and the accuracy of AUV location and feature location estimation can be improved to some extent by retaining more information carried by particles. The experimental results based on trial data show that the proposed simulated annealing variance reduction FastSLAM method avoids particle degradation, maintains the diversity of particles, weakened the degeneracy and improves the accuracy and stability of AUV navigation and localization system.