Abstract: In multi-beam sounding using reconstructed sound velocity profiles in the areas with significant variation of seawater properties, the complexity of shallow water and the stability of deep water are not taken into account for the function order selection of traditional empirical orthogonal function (EOF) method. Aiming at the problems of large computation amount and low accuracy of traditional EOF method, an approach to determining the orders of layered EOF for sound velocity profile reconstruction is presented in this paper. The depth is calculated by constant gradient ray tracing, and under the requirement of 0.25% depth difference, the effective beam ratio is counted and the reasonable orders are determined adaptively. The experimental results show that the proposed approach reduces the computational complexity and improves the accuracy compared with the sounding method using the traditional EOF-reconstructed sound velocity profile.