The invention relates to an underwater gas chromatography system for realizing in-situ test for H2 and CH4 in seawater and an operation method thereof. The underwater gas chromatography system comprises a seawater automatic sampling and gas membrane extracting unit, a multi-component gas automatic detecting and self-correcting unit and an exhaust gas recovering unit, wherein the seawater automatic sampling and gas membrane extracting unit is mounted on an instrument cabin end cover; the multi-component gas automatic detecting and self-correcting unit and the exhaust gas recovering unit are packaged in a high-pressure sealing instrument cabin; the seawater automatic sampling and gas membrane extracting unit is used for separating and extracting gas from a seawater sample and the gas is applied to the subsequent assay determination of a gas automatic detection device; the multi-component gas automatic detecting and self-correcting unit is used for quantitatively analyzing and determining the content of the gas in the seawater by using a pulse helium ionization detector; the exhaust gas recovering unit is used for storing the exhaust gas discharged from the system in an exhaust gas bottle, keeping the system pressure within a suitable numerical range and ensuring the normal running of all functional components in the system. According to the invention, the gas chromatographic technique is applied to underwater position and can be used for performing underwater accurate in-situ test on various dissolvable gases in deep sea and truly reflecting the content of the in-situ gases on seabed.