The point diffraction interferometer is a common instrument used in modern ultra-precision surface testing. It can be used in the sub-nanometer measurement because its reference wave is produced by pinhole diffraction instead of optic surface, which dramatically limits the measurement accuracy. A new calibration system, which can reduce the alignment difficulty and a new method that takes advantage of the background intensity of the interferogram to locate the CCD senser have been proposed. The experimental result indicates that the system error is 0.009λ, when the pinhole has a diameter of 3 μm.