Now it is a tedious work for clinicians to interpret the images acquired by wireless endoscopy system, and a viable solution is to construct a map, which is the two- dimensional representation of gastrointestinal (GI) tract, to reduce the redundancy of images and improve the understandability of them. But it is difficult for traditional wireless endoscopy system to realize image capture with wide field of view and so it is difficult to generate the map of GI tract. A wireless Micro-Ball endoscopy system makes the full view image capture possible. Then image registration is a key technology for constructing the map. This paper discusses and analyzes two key problems on image registration in detail for Micro-Ball endoscopy system. A two-threshold criterion is proposed for determining the possibility of valid registration between two images, and a MSE approach is also given out to appropriately decide the registration direction in the final step of registration process.