The invention discloses a methanol water hydrogen fuel cell power supply system and a control method thereof, and belongs to the technical field of fuel cells. The system comprises a fuel cell module,a hydrogen production module, a fuel supply module and a gas pressure stabilizing module, wherein the gas pressure stabilizing module comprises a buffer tank, a first pressure sensor arranged in thebuffer tank, a safety valve arranged on the buffer tank, a first electromagnetic valve connected with the buffer tank and a throttle valve, the buffer tank is respectively connected with the hydrogenproduction module and the fuel cell module, and the first electromagnetic valve is connected with the throttle valve in series. According to the invention, the gas pressure balance of the gas pressurestabilizing module is maintained through the safety valve and the first electromagnetic valve, and when the system needs to run continuously, automatic pressure relief or active pressure relief is conducted on the gas pressure stabilizing module, so that it is guaranteed that the gas pressure is within a balance range to maintain the continuous running of the system, and the system has the advantages of being capable of meeting the millisecond-level butt joint requirement, good in gas pressure and hydraulic pressure balance degree, long in system continuous running time, high in equipment cohesion and high in control precision.