The present invention relates to a double battery management system of an engine automatic start and stop vehicle. The double battery management system is provided with a starter; a first battery only used for power supply of the starter; a second battery used for power supply of loads of the whole vehicle; a generator used for power supply of the first battery and/or the second battery and the whole vehicle; a first battery sensor used for acquiring electric quantity information and charging/discharging information of the first battery; a second battery sensor used for acquiring electric quantity information and charging/discharging information of the second battery; a battery switching module used for switching connection/disconnection of the first battery, the second battery and a whole vehicle network; an engine control module used for controlling an engine; and a vehicle body control module used for controlling the battery switching module and performing information interaction with the engine control module, the first battery sensor and the second battery sensor.