The invention discloses a quantum communication ATP (array transform processor) precise tracking system with an optical axis self-calibrating function and a calibrating method thereof, aiming at overcoming the problem that the center of the quantum light emitting optical axis and the visual field center of the precise tracking camera are inconsistent owning to emitting vibration, on-track weight loss, thermal gradient and the like. The precise tracking system consisting of a pyramidal prism, a quick directing mirror, a CMOS (complementary metal-oxide-semiconductor) camera, a quantum emitting module, a color-separating piece and the like is adopted, and a path of strong light of other wavelength is introduced in the quantum emitting module by an optical fiber combiner and is used as a self-calibrating light. Before the instrument works, the self-calibrating light is introduced in the camera to form images by a track selector; the position of the mass center of light spot is calculated and is used as the visual axis center during tracking external target. The established inter-satellite or satellite-ground optical link can lead the ATP system to capture and precisely track the target at the receiving end and to exactly send the quantum signal to the receiving end along the optical link simultaneously, thus ensuring to successfully realize the spatial scale quantum communication.