An apparatus for measuring micro-cracks in a membrane electrode assembly includes a resistance measurement unit to measure variation in electrical resistance of the membrane electrode assembly while tensioning the membrane electrode assembly in a state in which power is applied to an upper catalyst layer while a lower catalyst layer is insulated, an image capture unit to capture an image of micro-cracks in the upper catalyst layer while the membrane electrode assembly is being tensioned, and a controller to detect, in real time, variation in electrical resistance measured by the resistance measurement unit, corresponding to the image of micro-cracks captured by the image capture unit, and to interpret the size of the micro-cracks generated in the membrane electrode assembly based on the detected variation in electrical resistance.