The invention discloses an MEMS (Micro-Electromechanical Systems) methanol reforming fuel cell system, belongs to the field of methanol reforming fuel cells and aims to solve the problems of a traditional methanol reforming fuel cell system. The MEMS methanol reforming fuel cell system comprises a shell, a liquid storage bottle, an MEMS methanol reformer, an MEMS proton exchange membrane fuel cell, an MEMS air-liquid pump, a bi-directional valve, a lithium cell, a managing system, a left side fan and a right side fan, wherein the shell is in a cuboid shape, the liquid storage bottle is arranged on the outer surface of the back side of the shell, the MEMS methanol reformer, the MEMS proton exchange membrane fuel cell, the MEMS air-liquid pump, the bi-directional valve, the lithium cell, the managing system, the left side fan and the right side fan are arranged in the shell, an input port of the MEMS methanol reformer is communicated with a methanol outlet of the liquid storage bottle by virtue of a pipeline, the MEMS air-liquid pump and the bi-directional valve are arranged on the pipeline, an output port of the MEMS methanol reformer clings to an anode input port of the MEMS proton exchange membrane fuel cell tightly, and the contact position is sealed by a sealing material.