A natural gas hydraulic compression cylinder comprises a compression cylinder shell. A gas inlet and outlet opening is formed in the upper end of the compression cylinder shell, and a liquid inlet and outlet opening is formed in the lower end of the compression cylinder shell. An inner cavity of the compression cylinder shell is in sliding fit with a vertically-moving movable separation plate used for isolating a gas medium from a liquid medium. The inner cavity of the compression cylinder shell is divided by the movable separation plate into a gas compression cavity and a liquid expansion cavity. The volume of the gas compression cavity and the volume of the liquid expansion cavity relatively change along with vertical movement of the movable separation plate. When hydraulic oil injected in the compression cylinder compresses natural gas, the two media are not in contact, the phenomenon that the oil and the gas are mixed is avoided, the purity of the compressed natural gas can be improved, environment pollution can be avoided, and the safety of the work environment is improved.