A hydrogen generator comprising: a reformer for generating a hydrogen-containing gas through a reforming reaction of a raw material gas and water; a raw material supply unit for supplying the raw material gas; a raw material flow measuring unit for measuring a flow of the raw material gas; a first temperature detector for detecting a temperature of the reformer; a combustor for combusting at least one of the raw material gas and the hydrogen-containing gas which are combustible gases by using air to heat the reformer; a removing unit (8, 9) for removing carbon monoxide from the hydrogen-containing gas through a reaction of carbon monoxide and a reactant gas; a reactant gas supply unit (13, 14) for supplying the reactant gas; and a control unit; wherein the control unit is configured to control an amount of the raw material gas supplied from the raw material supply unit such that a first detection temperature detected by the first temperature detector reaches a predetermined temperature, and to control an amount of the reactant gas supplied from the reactant gas supply unit (13, 14), based on the flow of the raw material gas which is measured by the raw material flow measuring unit, during control of the amount of the raw material gas, wherein the removing unit (8, 9) includes a shift converter for converting carbon monoxide by using steam, and a selective oxidization unit for oxidizing carbon monoxide by using an oxidizing gas; and wherein the reactant gas supply unit (13, 14) includes a steam supply unit for supplying the steam, and an oxidizing gas supply unit for supplying the oxidizing gas, the hydrogen generator further includes a storage section for storing a measurement flow of the raw material gas during an operation of the hydrogen generator; characterized in that the control unit is configured to set a reference flow of the raw material gas based on the measurement flow of the raw material gas stored in the storage section, and to control at least one of a supply amount of the steam and a supply amount of the oxidizing gas based on a result of comparison between the measurement flow of the raw material gas and the reference flow. a reformer for generating a hydrogen-containing gas through a reforming reaction of a raw material gas and water; a raw material supply unit for supplying the raw material gas; a raw material flow measuring unit for measuring a flow of the raw material gas; a first temperature detector for detecting a temperature of the reformer; a combustor for combusting at least one of the raw material gas and the hydrogen-containing gas which are combustible gases by using air to heat the reformer; a removing unit (8, 9) for removing carbon monoxide from the hydrogen-containing gas through a reaction of carbon monoxide and a reactant gas; a reactant gas supply unit (13, 14) for supplying the reactant gas; and a control unit; wherein the control unit is configured to control an amount of the raw material gas supplied from the raw material supply unit such that a first detection temperature detected by the first temperature detector reaches a predetermined temperature, and to control an amount of the reactant gas supplied from the reactant gas supply unit (13, 14), based on the flow of the raw material gas which is measured by the raw material flow measuring unit, during control of the amount of the raw material gas, wherein the removing unit (8, 9) includes a shift converter for converting carbon monoxide by using steam, and a selective oxidization unit for oxidizing carbon monoxide by using an oxidizing gas; and wherein the reactant gas supply unit (13, 14) includes a steam supply unit for supplying the steam, and an oxidizing gas supply unit for supplying the oxidizing gas, the hydrogen generator further includes a storage section for storing a measurement flow of the raw material gas during an operation of the hydrogen generator; characterized in that the control unit is configured to set a reference flow of the raw material gas based on the measurement flow of the raw material gas stored in the storage section, and to control at least one of a supply amount of the steam and a supply amount of the oxidizing gas based on a result of comparison between the measurement flow of the raw material gas and the reference flow.