The invention discloses an unmanned ship energy management method and system. The method includes the following steps that: a permanent magnet synchronous motor is utilized to drive the propeller of an unmanned ship to operate; and direct-current electric energy outputted by a storage battery and a super-capacitor is converted into alternating-current electric energy, so that the alternating-current electric energy can be supplied for the permanent magnet synchronous motor. According to the method, in the power supply period of the storage battery and the super-capacitor, an energy distribution process is performed through the following manners that: when the permanent magnet synchronous motor is started, a first switch connected with the positive pole of the storage battery is controlled to maintain a normally-opened state, and a second switch connected with the positive pole of the super-capacitor is controlled to maintain a normally-opened state, so that direct-current electric energy can be outputted; and when the starting of the permanent magnet synchronous operates to a preset start time, the on-off sequence of the first switch and second switch is adjusted, so that the output current ie of the storage battery can be equal to ce(t)iqref, and the output current ic of the super-capacitor can be equal to cc(t)iqref. According to the unmanned ship energy management method and system of the invention, the output energy of the storage battery and the super-capacitor is reasonably distributed, so that the acceleration performance of the electric unmanned ship can be effectively improved, and the requirements of high energy density and high power density of the electric unmanned ship can be satisfied.