The present invention discloses a method and a system for measuring flow layer velocities using correlation velocity measuring sonar. The present invention provides a new theoretical expression for fluid medium sonar array temporal and spatial correlation function, the velocities of each flow layer are derived by fitting experimental data and a theoretical function, or fitting absolute value operated and localized experimental data and a theoretical function. The fluid medium sonar array temporal and spatial correlation function of the present invention is succinctly expressed by Kummer function, and well coincided with the experiments. This function is applicable not only to far field region, i.e. planar wave region, but also Fraunhofer region, i.e. spherical wave region. The present invention has the merits of high measurement accuracy, small calculation load, good robustness and fast convergence.