The invention relates to a control method and a system for an electronic load regulator of a generator. The method includes: measured frequencies and control parameters of a plurality of virtual water tanks are respectively obtained in real time, deviation values of the virtual water tanks are calculated and obtained according to the measured frequencies and a received control frequency, and control steps of the virtual water tanks are calculated and obtained according to the deviation values and the control parameters; the total control step of a load water-resistance tank is calculated according to the control steps of the virtual water tanks, the silicon controlled rectifier control step of the electronic load regulator is calculated, obtained, and outputted, and frequency stable regulation of three-phase current is realized; the current value and the frequency value of the three-phase current of the generator are obtained, a given value of the three-phase current of the generator is calculated, obtained, ad outputted according to the current value and the frequency value of the three-phase current, and the balance of the three-phase current of the generator is controlled. According to the method and the system, the electronic load regulator is controlled via frequency balance and current balance, three-phase imbalance due to load change is prevented, and the usage security of the generator is improved.