A method and a system for measuring the velocity of a vessel relative to the bottom using a velocity measuring correlation sonar are disclosed. The present invention provides a new theoretical expression for the bottom medium sonar array temporal and spatial correlation function. The velocity of the vessel relative to the bottom is derived by fitting experimental data to a theoretical function. The bottom medium sonar array temporal and spatial correlation function of the present invention is succinctly expressed in zero-rank Bessel function, and well coincided with experiments. The function is applicable not only to far field region, i.e. planar wave region, but also to Fraunhofer region, i.e. spherical wave region. Transmit transducers and receive transducers are multistatic in the velocity measuring correlation sonar of the present invention, so the transmit beam width and the receive beam width can be selected reasonably. The present invention is applicable to measuring the velocity of the vessel relative to the bottom with high measurement accuracy, small calculation load, good robustness and fast convergence.