Disclosed herein is a method of detecting defects of a fuel cell membrane-electrode assembly which comprises a gas diffusion layer, a catalyst layer and an electrolyte membrane. The method includes steps of: supplying gas to a first side of the membrane-electrode assembly; deducing a pressure of the supplied gas and a permeation rate of the gas permeating to a second side of the membrane-electrode assembly and then deducing an interface pressure between the electrolyte membrane and the gas diffusion layer of the membrane-electrode assembly using the deduced pressure of the supplied gas and the permeation rate; calculating a gas permeability of the electrolyte membrane using the deduced values of the pressure of the supplied gas and the permeation rate and a predetermined outlet pressure at the second side of the membrane-electrode assembly; and determining a defect state of the electrolyte membrane using a variation in the calculated gas permeability according to a change in the pressure of the supplied gas.