Film diffractive optical elements have the characteristics of low surface mass density and loose surface shape tolerance. Large aperture diffractive telescope system with film diffractive optical element as the primary lens, as the optical payload with super large aperture, light quality and high etendue, has much more ability to observe earth real time and undisturbed. In this paper, the fabrication tolerance of the diffractive element and relative position tolerance of the two parts of the diffractive telescope system were analyzed. A measuring method of the relative position of the two parts of the diffractive telescope system was proposed and the measuring accuracy was analyzed. This method can form two spots on the CMOS active detectors with laser source using two computer-generated holograms (CGH) elements of different structures. The center deviation and tilt can be measured exactly by analyzing the relative position of the two spots real time. The measuring accuracy can achieve 50 μm and 0.003° respectively. These critical technologies lay the foundation for the implementation of the large aperture diffractive telescope system in the future.