In order to carry out reaction smoothly, a measure and control system of an onboard micro-channel reactor for hydrogen production via methanol steam reforming is developed. A subsystem of temperature control is designed to measure and control the temperatures of reactor and evaporator. Flow control subsystem, including liquid flow control of reactant and mass flow control of reducing gas, is also developed. Virtual instrument technology and graphical programming language LabVIEW are applied to integrate all the control functions in a single program, which makes it convenient for operation and further development. The experimental results validate that the reaction can be carried out successfully under the control of this measure and control system.