The invention provides a small-sized long-endurance fixed-wing unmanned aerial vehicle power supply controller system and a running method. The small-sized long-endurance fixed-wing unmanned aerial vehicle power supply controller system comprises a rectification voltage stabilizing module, an interval power generating module and a power supply switching module; three-phase alternating current generated by a power generator is converted to direct current required by unmanned aerial vehicle airborne electronic control equipment by utilizing a three-phase rectification bridge, and the voltage isstabilized in a certain range; the interval power generating module comprises a frequency-to-voltage module and a voltage-to-switching value module which jointly control and decide the function that whether an engine generates power or not in different frequency interval sections; and the power supply switching module realizes switching of power supplying sources of the unmanned aerial vehicle airborne equipment. The small-sized long-endurance fixed-wing unmanned aerial vehicle power supply controller system aims to supply power for the airborne electronic control equipment by utilizing the engine to generate power, meanwhile, a complicated single ship computer is not expected to be introduced for controlling, the rotating speed of the engine can be distinguished only through hardware design, power supplying in a suitable interval is achieved, and smooth switching between power supplying by a storage battery set and power supplying by the power generator is achieved.