The disclosure relates to a method for making fuel cell system. The fuel cell system includes a fuel cell module curved to form a chamber. The fuel cell module includes a container having a number of through holes and a membrane electrode assembly located on the container and cover the number of through holes. The membrane electrode assembly includes a proton exchange membrane having a first surface and a second surface opposite to the first surface, a cathode electrode located on the first surface and an anode electrode located on the second surface. A fuel cell module is at least partially immerged in the fuel and the oxidizing gas is supplied in to the chamber of the fuel cell module.