The invention discloses a zero-carbon-emission hydrogen production system by methanol water reforming and application and a hydrogen production method thereof. The hydrogen production system comprises a methanol water storage vessel, a delivery pump, a first heat exchanger, a reformer and a carbon dioxide recovery device, wherein the reformer is provided with a reforming chamber, an electromagnetic heater and a hydrogen purification device; the electromagnetic heater provides heat energy for the reforming chamber; the reforming chamber is used for hydrogen production reaction of methanol and water by reforming to obtain carbon dioxide and hydrogen; carbon dioxide and hydrogen are mixed with water vapor to form high-temperature mixed gas, and the high-temperature mixed gas is delivered into the hydrogen purification device; after purification and separation, hydrogen is delivered out, at the same time carbon dioxide and unreacted water vapor mixed gas are also delivered out, and then carbon dioxide and unreacted water vapor mixed gas are delivered into the carbon dioxide recovery device after passing through the first heat exchanger; the carbon dioxide recovery device is a replaceable modular carbon dioxide recovery device and used for recovering carbon dioxide and part of the water vapor. The zero-carbon-emission hydrogen production system provided by the invention can recover carbon dioxide, has no impact on the environment and causes no harm to the hydrogen production system self and is beneficial for popularization and application in the field of new energy resources such as fuel cell cars.