A reformer for a fuel cell system, a fabrication method thereof, and a fuel cell system are provided. The reformer includes a plurality of reaction substrates. The reaction substrates each have a reaction substrate body provided with a flow channel with micropores formed on the surface of the flow channel. In addition, a catalyst layer may be formed within the flow channel of the reaction substrate body. Since the reformer for a fuel cell system suggested in the present invention includes reaction substrates having micropores formed in the flow channel, it has a high specific surface area and high catalyst activity. Moreover, since the catalyst layer is formed by a deposition method, the reformer can be of a small proportion, occupying little space in the fuel cell system.