The invention relates to a photovoltaic system intelligent complemented charging and discharging method. This system comprises a solar energy battery unit, a storage battery, an input electric switch,an output electric switch, loads and so on. A group of storage battery in the solar energy photovoltaic system is shunt-wounded by using two groups of original system storage batteries with 1/2 capacity; the solar energy battery uses the charging controller to process impulse charging for the two groups of batteries; firstly, the impulse current charges the group of battery; during the charging diapause, the impulse current charges another group of battery, circulating in this way, power of the solar energy is 100% used. The two groups of storage batteries can process impulse discharging, forming intelligent complementally charging and discharging. This method can improve maintaining condition of the storage battery and release the erosion of the facilities by acid mist and pollution forthe environment, enhancing the capacity converting rate; the two groups of storage batteries can alternatively discharge and maximally strengthen using rate of the storage battery, prolonging using age of the storage battery.