The invention discloses a battery encryption system based on the asymmetric cryptographic algorithm, and relates to the technical field of battery encryption. The battery encryption system comprises abattery unit, a vehicle unit and a cloud end server. The battery unit is in wire communication with the vehicle unit through serial communication, and the vehicle unit is in wireless communication with the cloud end server through a wireless transmitting module. The battery unit comprises an encryption IC and a first main control chip, and the first main control chip is in communication with theencryption IC through an I2C communication module. The vehicle unit comprises a serial port module, a second main control chip and a wireless module, and the second main control chip is in wireless communication with the serial port module and the wireless module. According to the battery encryption system based on the asymmetric cryptographic algorithm and the method thereof, all produced batterypublic keys are corelated with the battery unique serial number and need to have the backups on the server, and thus the situation that a counterfeiter purchases the same model of IC or breaks the single battery, and then replicates a large amount of broken batteries so as to hide from authentication can be prevented.