A charging system, a charging method, and a mobile terminal based on dual batteries are provided. The charging system based on dual batteries includes a main board and a backup battery; the main board has a main charging chip and a main battery arranged thereon; the backup battery has a secondary charging chip and a secondary battery arranged thereon. The main board further includes a USB connector configured to connect to a charger, and a switch configured to switch to a corresponding charging path based on an inserting state of the backup battery. When the backup battery is inserted, the main charging chip is controlled to charge the main battery, and the secondary charging chip is controlled to charge the secondary battery simultaneously. When the backup battery is pulled out, the main charging chip is controlled to charge the main battery.