A pinhole detection system of a fuel cell element unit including a density measurement module that calculates a density of a fuel cell element unit using weight and volume data measured from electronic weight balance and 3D scan type volume integrator. Photon energy ranges of X-ray beam and window species of the pinhole detection system automatically are selected from Group 1 or Group 2 according to the density reference point for a fuel cell element, and a stage on which a fuel cell element unit is disposed to be detected. A drive portion that moves the stage to rotate the fuel cell element unit. An X-ray source is disposed at one side of the stage to apply X-ray to the fuel cell element unit that rotates. An image detector detects an X-ray penetrating the fuel cell element unit, and a computer tomography that reconstructs a three dimensional tomogram.