Considering the low precision of low-resolution image used for the registration process, a sub-pixel image registration method based on super resolution reconstruction was put forward. Firstly,10 times down-sampling was carried out in the image sequence with 1~9 pixel displacement to obtain an image sequence with 0.1~0.9 sub-pixel displacement; then, a mathematical model was built in accordance with the image acquisition process, and Maximum A-Posteriori (MAP) method was used to carry out super resolution reconstruction in low-resolution image of the sub-pixel displacement to obtain high-resolution image based on the Bayes Theory; finally, the extended phase correlation method with sub-pixel registration accuracy was applied to conduct image registration. The registration and noise experiments inclicate that the maximum registration error is 0.03 pixel. The proposed method has high registration accuracy and strong anti-noise ability. It can realize the sub-pixel registration for low-resolution image, at the same time, it can meet the requirements for high-accuracy registration of visible image and infrared image.