An adaptive power supply system for an unmanned vehicle and an operation method thereof are provided. The adaptive power supply system includes an adaptive power supply, a battery, a sensing circuit, and a power dispatch controller. The output terminal of the adaptive power supply powers the load circuit of the unmanned vehicle. The battery is coupled to the output terminal of the adaptive power supply. The sensing circuit senses the output of the output terminal of the adaptive power supply and the output of the battery. The power dispatch controller controls the output of the output terminal of the adaptive power supply according to the sensing result of the sensing circuit. The power dispatch controller determines whether one or both of the adaptive power supply and the battery power the load circuit by adjusting the output of the adaptive power supply.