A modular fuel cell structure includes an anode conductive sheet, an air electrode sheet, a separating membrane, and a cathode conductive sheet stacked on a casing. The casing has a reaction vessel, and also has a first, a second, and a third flow passages, which all communicates with the reaction vessel, and are all independent. Said modular structure forms a fuel cell system with a first storage tank, a second storage tank, a retrieval device, and a feeding device which controls the first and the second storage tanks to deliver a first and a second materials to the casing. The first and the second materials are respectively injected into the reaction vessel for reaction through the first and the second flow passages, and then exhausted to the retrieval device through the third flow passage after the reaction. With the independent flow passages, the efficiency of power generation could be improved.