A set of calibration system for multi-beam sonar is designed by the principle and method of underwater acoustic metrology. Using the multi-dimensional operation control device, the calibration for acoustical index is completed in the anechoic pool, including the sound source level and beam width. The calibration for geometrical index is carried out in the large scale and deep-water prototype pool, including the bathymetric accuracy. Components and method of the calibration system are introduced, as well as the expanded uncertainty of the calibration system is presented. By comparing the calibrating value and the indicating or nominal value of the detected multi-beam sonar, test results show that the sound source level error is less than 0.7dB, the beam width indication error is less than 10% and the bathymetry value error is less than 0.2%.