An atmospheric-pressure microwave plasma torch is employed to generate hydrogen by injecting methanol aerosols into the near afterglow region of a nitrogen microwave plasma. Two types of reaction chambers are proposed to study the influence of different boundary conditions of reaction chambers on hydrogen production by comparison. Fourier transformation infrared spectrometer and gas chromatography are used to measure and determine the hydrogen production rate, energy efficiency, and hydrogen yield. Also, the effects of conditions of methanol injection and discharge parameters on methanol decomposition are investigated, respectively. It is found that the active species originated from collision with the excited and ionized N2 in the high gas temperature in the plasma discharge plays an important role in the conversion of methanol to hydrogen. The gas flow pattern in the reaction chamber is closely related to boundary conditions and significantly affects the reaction time of methanol in it, which is analyzed with the software of computational fluid dynamics. The achievements of hydrogen production in our work are as follows: production rate up to 921 l/h, energy yield up to 371 l/kWh, and hydrogen yield up to 70%, respectively. Furthermore, the reaction mechanism is discussed in detail with respect to the formation of outlet products.