The traditional method would take a long time in the process of frequency response compensate in wideband microwave spectrum analyzer,and was not beneficial to produce spectrum analyzer on a large scale. So it should be improved to increase efficiency. First,analyzes the reason why the process of frequency response compensatespends longer time from three aspects; second,proposes the relative improvement measures: change the switch order of frequency point in frequency response compensate system, increase the execution efficiency of remote control commands, judge the stable state of output power dynamically of signal source after the frequency point was switched. It is proved that after the traditional method of frequency response compensate was improved, compensate time greatly reduced, and the efficiency has significantly increased.