In order to solve the problem of close range image registration of multi-source image fusion system with a separate optical axis structure, a registration model of binocular imaging system was established to analyze the impact of the lens center distance on the registration accuracy. The incidence angle difference of object points to different lenses was considered in this model, which determined the registration accuracy. In this way, the relationships of registration accuracy, lens center distance and object distance were analyzed. Finally, considering the angular resolution of detectors and optical axis calibration accuracy, computational formula of the distance range of pixel-level registration of separate optical axis system was given, which could be adjusted for variable close range image registration by the initial angle of two optical axes and the pixel translation of the image. Calculation results indicate that the separate optical axis system can achieve pixel-level registration from a closest distance to infinity, when the optical axes are parallel. If the system is adjusted to register for a closer distance, the registration range will become finite. Smaller lens center distance and higher optical axis calibration accuracy will help to expand the registration range. Finally, with the calculated registration range and the measured target distance, the variable close range image registration of infrared and visible light image fusion system with separate optical axis structure has been achieved.