NOVELTY - A hydrogen generator (100) has raw material supply device (101), modifier (111), transformer (121), temperature detectors (113,123), heater (112), cooler (122) and controller (200). Modifier modifies raw material to produce hydrogen-containing gas. Transformer contains transformation catalyst, and reduces carbon monoxide in hydrogen-containing gas. Temperature detector detects temperature of transformation catalyst. Controller controls raw material supply device such that interior of transformer is purged with raw material, when detected temperature is less than threshold value.    USE - Hydrogen generator is used in fuel cell system (claimed).    ADVANTAGE - The performance degradation of transformation catalyst is effectively suppressed.    DETAILED DESCRIPTION - A hydrogen generator has a raw material supply device for supplying a raw material, a modifier, a transformer, temperature detectors (113,123), a heater for heating modification catalyst, a cooler for cooling transformation catalyst and a controller (200). The modifier contains modification catalyst, and carries out modification reaction of raw material to produce hydrogen-containing gas. The transformer contains transformation catalyst, and reduces carbon monoxide contained in hydrogen-containing gas by shift reaction. The temperature detectors (113,123) detect the temperature of transformation catalyst and modification catalyst. The controller controls raw material supply device such that interior of transformer is purged with raw material, when detected temperature of modification catalyst is less than threshold value at which deterioration of modification catalyst by raw material is prevented at the time of termination of operation. The cooler is controlled such that detected temperature of transformation catalyst is less than threshold value at which deterioration of transformation catalyst is suppressed. An INDEPENDENT CLAIM is included for operating method of hydrogen generator.    DESCRIPTION OF DRAWING(S) - The drawing shows the schematic structure of fuel cell system.    Hydrogen generator (100)    Raw material supply device (101)    Modifier (111)    Heater (112)    Temperature detectors (113,123)    Transformer (121)    Cooler (122)    Controller (200)