The invention discloses an online high-purity hydrogen preparation system for a fuel cell. The online high-purity hydrogen preparation system comprises a methyl alcohol box as well as a raw material box and a catalytic burner which are connected with the methyl alcohol box through a methyl alcohol metering pump, wherein a fuel cell discharge water inlet is formed in the raw material box, an oxygen inlet is formed in the catalytic burner, an ethanol water metering pump and a heat exchanger are sequentially connected onto the raw material box, a vaporizer is connected onto the heat exchanger, a reforming reactor is connected onto the vaporizer, a palladium film purifier is connected onto the reforming reactor, and the palladium film purifier is connected with the catalytic burner; the invention further discloses a control method of the system. According to the system provided by the invention, online hydrogen supplying is performed through a manner of using a methanol water reforming reaction to produce hydrogen, the yield of pure hydrogen is controlled through adjusting the flow of an ethanol water mixture; the method has the characteristics of high hydrogen storage density, high hydrogen purity, low energy consumption, compact structure, simpleness and convenience in start-stop controlling, easiness in implementing modular design and the like.