In order to reduce the costs, improve the performances and promote the industry process, basing on calculus and finite element thinking, conceptual design of special-shaped membrane electrode assembly (S-MEA) was proposed, including six shapes. S-MEA size was determined by calculating, admeasuring and devising elaborately, whose basic parameter was gained from experiment datum. S-MEA was made up of titanium mesh anode layer, anode catalyst layer, Nafion membrane layer, cathode catalyst layer, gas diffusion layer and titanium mesh cathode layer in turn, which was different from MEA of the fluid field bipolar plates in the macro-structure but had the same micro-mechanism. Three-dimensional model was devised through Pro/E, planar diagrammatic drawing was created by the software also, and detail drawing was designed further with CAD. The process of preparing S-MEA was researched basing on the design. Then three typical S-MEA prototypes were made by bend-hot-pressing with home-made molds and precision hydraulic machine, including open triangular cross-section MEA, circular cross-section MEA and square cross-section MEA.