The invention discloses a method, system and device for controlling the frequency of a wireless charging system and a storage medium. The method comprises the steps of correspondingly setting an information variable containing master frequency information and an information variable containing slave frequency information as a master phase observation variable and a slave phase observation variablerespectively; operating secondary side equipment at the initial frequency, and respectively sampling the master phase observation variable and the slave phase observation variable; setting a startingpoint of observation, and determining the size relationship between the current master frequency and the current slave frequency according to the master-slave phase information within a preset time from the starting point; and adjusting the size of the current slave frequency according to the size relationship so as to enable the current slave frequency to track the current master frequency. According to the invention, two information variables respectively containing the master and slave frequency information are selected, the relationship between the two frequencies is judged according to the phases of the information variables, and then frequency modulation is carried out, so that the two frequencies are enabled to be the same or similar, primary and secondary side communication or auxiliary coil addition is not needed, engineering application scenes are satisfied, and the engineering and the system stability are realized.