An S-band 45 MW pulsed klystron is developed in Institute of High Energy Physics (IHEP).This klystron is a modified version of the existing 30 MW tube, which produces 45 MW at a 320 kV beam voltage by optimizing the focusing magnetic field. Therefore, the focusing coil needs to be re-arranged and its supporting structure is newly designed to meet 45 MW klystron demands. This paper describes the design, manufacture and operation of the focusing magnet system. The results of the magnetic field, the high power of the tube are presented. The operation status of the focusing magnet system is also included. The high power test results of the prototype tube show that the design, the manufacture and the operation of the focusing magnet system are successful.