The invention discloses a multiple waveguide output structure for a gyrotron amplifier, which comprises a composite cavity, a plurality of rectangular coupling holes, a first vertical wall, a second vertical wall, a high-order mode circular waveguide, a smaller circular waveguide, a plurality of rectangular coupling holes and a plurality of output waveguides, wherein the composite cavity comprises an internal cylindrical cavity and an external coaxial cavity which are in a coaxial line, the internal cylindrical cavity is isolated from the external coaxial cavity through a common wall, the rectangular coupling holes are cyclically arranged on the common wall and the external wall of the external coaxial cavity, the first vertical wall and the second vertical wall are positioned at both ends of the axial direction of the internal cylindrical cavity and the external coaxial cavity and are mutually vertical to the common wall, the high-order mode circular waveguide is connected to the first vertical wall, the smaller circular waveguide is connected to the second vertical wall, and the output waveguides are coupled with the rectangular coupling holes in the external coaxial cavity. The invention realizes the transformation from a millimetric wave band high-order mode to a single basic-order mode operation, solves the problem of insufficient capacity of single waveguide output power, improves the capacity of output power, is suitable for the linearly polarized output of the basic-order mode and effectively inhibits the oscillation of a spurious mode at the same time.