A hydrogen generating apparatus composed of an autothermal-reforming catalyst layer, a conduit pipe for feeding a mixture of methanol and steam, a conduit pipe for feeding oxygen equipped with a flow regulator, and a hydrogen-permeable membrane disposed downstream of the autothermal-reforming catalyst layer. The hydrogen generating apparatus is equipped with a temperature-measuring device for measuring the temperature of the hydrogen-containing gas discharged from the autothermal-reforming catalyst layer. The amount of oxygen to be fed to the autothermal-reforming catalyst layer is increased or decreased by the flow regulator according to the measured temperature of the hydrogen containing gas. Thus, the heat generation by the autothermal reforming is controlled and the temperature of the hydrogen containing gas is regulated within a limited range so as to maintain the hydrogen separation step at an optimum temperature. With the hydrogen generating apparatus, the heat generated by the autothermal reforming reaction is effectively utilized in the hydrogen separation step without needing an additional means.