The invention discloses a method and a system for measuring a volume of a microcavity of a fuel rod. The system comprises a clamping part, a standard container, a vacuumizing device, a pressure measuring device and a plurality of contrast seal parts. The clamping part comprises a cavity with an opening, the cavity is used for mounting of the fuel rod or the contrast seal parts, and a seal component is arranged on the side wall of the cavity and used for sealing a gap between the cavity and a to-be-measured element or the contrast seal parts mounted in the cavity. An air guide pipe is arranged on the clamping part which is internally provided with a passage A, the cavity and the air guide pipe are communicated through the passage A, the air guide pipe is connected with the pressure measuring device, the standard container and the vacuumizing device through pipelines respectively, and a valve is arranged on the pipeline through which the air guide pipe is connected with the standard container. The method and the system for measuring the volume of the microcavity of the fuel rod have the advantage that volume measurement of postirradiation internal cavities of rod cluster type fuel elements is realized by establishment of a microvolume measurement correction factor calibration method and a technique for measuring volumes of postirradiation internal cavities of fuel rods.