Provided are a hydrogen purification device protection system and method based on a methanol-water reforming hydrogen production system. The protection system comprises a reformer (1), a methanol-water storing and transporting subsystem (4), a vacuumizing and air discharging subsystem (5), and a non-hydrogen and non-oxygen protection gas conveying subsystem (6). The reformer (1) comprises a reforming chamber (101) and a hydrogen purification device (102). The reforming chamber (101) is used for allowing methanol and water steam to be subjected to a reforming reaction to prepare a mixed gas of hydrogen and carbon dioxide. The hydrogen purification device (102) is used for separating the prepared mixed gas of hydrogen and carbon dioxide. The methanol-water storing and transporting subsystem (4) is used for transporting methanol and water raw materials to the reforming chamber (101) of the reformer (1). The vacuumizing and air discharging subsystem (5) is used for pumping air in pipelines of the reforming chamber (101) and the hydrogen purification device (102) out when the hydrogen production system stops working. The non-hydrogen and non-oxygen protection gas conveying subsystem (6) is used for reversely filling a non-hydrogen and non-oxygen protection gas into the hydrogen purification device (102) when the methanol-water reforming hydrogen production system stops working. In the protection system, by reversely filling the non-hydrogen and non-oxygen protection gas into the hydrogen purification device (102), gases such as hydrogen in the hydrogen purification device (102) are quickly removed, and accordingly the hydrogen purification device (102) is protected.
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