Marine channel measurement is of great significance to ensure the reliable operation of ships. Currently, the system used in anomaly measurement is only one of the time or spatial correlation of measurement errors. Considering the shortcomings of the existing single-beam multi-beam bathymetric system (SBMBBS) and the spatio-temporal correlation of the error matrix, a method of ocean channel measurement is proposed based on the single-beam multi-beam bathymetric system. In this system, the dimension reduction ability of ocean channel measurement and the multi-scale modeling ability of wavelet transform are fully utilized to construct the measurement error system. In the analysis of residual error, it is mainly achieved through control charts. In addition, the sliding window mechanism is effectively used to realize the ocean channel measurement of single-beam multi-beam bathymetry system, from which an on-line SBMBS is obtained. Through the analysis of the measured data and the simulation results, it can be concluded that compared with the BSA algorithm and KLE algorithm, SBMBBS algorithm has more prominent advantages and better measurement performance. The results show that the measurement performance of the online SBMBBS algorithm is very close to that of the SBMBBS algorithm, and requires a very short one-step execution time, which meets the requirements of ocean channel measurement.