In order to solve the problem of multi pieces of TDI CCD stitching pixel mismatch in satellite flexible transformation multimodal imaging, a kind of pixel matching algorithm which can realize overlapping and displacement pixel fast assembly and registration of TDI CCD camera is proposed. Through the analysis of multi pieces of TDI CCD assembly imaging pixel mismatch phenomenon caused by the variation of image motion velocity vector in focal plane during the process of satellite side swing imaging, the imaging velocity vector ray tracing and the homogeneous coordinate transformation method is designed. Based on this method, the image motion velocity and drift angle which influence image mismatch during the process of satellite side swing imaging and the number of pixel in direction of longitudinal displacement and transverse overlapping of two pieces of TDI CCD assembly imaging are calculated. Three-axis air flotation turntable attitude simulation system and a TDI CCD camera are used in experiment to verify the pixel matching algorithm of two pieces of TDI CCD assembly imaging. TDI CCD camera of viewing angle of 10°, after an assembly period, the original number of longitudinal displacement and transverse overlapping pixels of two pieces of TDI CCD assembly imaging turns from 148.5 and 50 to 137 and 49, respectively, which is consistent with theoretical result in longitudinal displacement direction and has a deviation of only 0.1 pixel in transverse overlapping direction. Compared with the theoretical and experimental result, the design of fast registration algorithm of calculation of longitudinal displacement and transverse overlapping pixel can solve the accuracy of TDI CCD assembly imaging, which guarantees image pixel matching and obtain high quality images.