Abstract: To solve the problems of non-concentric array and large computational cost in position restoration algorithm in multibeam bathymetry system, a non-concentric array algorithm based on minimum distance constraint is proposed, in which, the minimum distance constraint problem is constructed, and the bathymetry point is calculated by Newton’s method and quickly iteratively corrected according to the actual acoustic signal propagation time. On the basis of the propagation surface position restoration algorithm, a fast algorithm for non-concentric arrays based on matrix rotation is proposed, which solves the vector by rotating vector instead of equation, uses the sound line tracking based on polynomial fitting to quickly solve the bathymetry point, and updates the iteration interval by the spatial distance error. A theoretical accuracy evaluation method for position restoration algorithm under non-concentric array model is established. Simulation results show that the average theoretical error of the two algorithms is less than 0.001 m, which reduces the amount of computation by 98.12% and 99.50% under the same high precision conditions compared with the propagation surface multi-beam footprint restoration algorithm. The fast algorithm for non-concentric arrays based on matrix rotation algorithm is applied to the domestic multi-beam bathymetry equipment, and the data of 121 pings per second is calculated, and the average difference between the bathymetry results and the Kongsberg ME122 bathymetry results is 2‰ water depth value, which indicates that the algorithm has good engineering application value.