The invention discloses a cryogenic separation system for separating a mixed gas. The system mainly comprises two parts, that is, a molecular sieve purification unit and a cold box of a cryogenic separation device, wherein the mixed gas at least containing carbon monoxide, hydrogen, methane and a small amount of nitrogen communicates with an inlet pipeline of the molecular sieve purification unit, the molecular sieve purification unit sequentially communicates with a first main heat exchanger, a tower bottom reboiler of a stripping tower, a tower bottom reboiler of a demethanizing tower, and a second main heat exchanger in the cold box of the cryogenic separation device through a first pipeline and then is connected to a middle inlet of a hydrogen separation tank after impurities easy to condense at a low temperature, of carbon dioxide, methyl alcohol and water, are removed, and three hydrogen-enriched gas pipelines are connected out from the top of the hydrogen separation tank and communicate with an external hydrogen-enriched gas collection system after a hydrogen-enriched gas is reheated by the two main heat exchangers to recover a cold quantity; and two liquid pipelines are connected out from the bottom of the hydrogen separation tank, one liquid pipeline communicates with a middle inlet pipeline of the stripping tower through a first throttle valve and the second main heat exchanger, and the other liquid pipeline communicates with an upper inlet pipeline of the stripping tower through a second throttle valve.