With the development of UAVs in agricultural applications, multi-spectral cameras are designed to be installed on these platforms in small size and weight to help users for applications. These cameras are designed in multi lenses structure each lens considered for each spectral band. Band miss-registration of low altitude multispectral images acquired via UAVs is challenging due to multi view image sensors and optics structure of the multispectral cameras. In this study, an image based registration method is proposed to reduce the effect of relief displacement on miss-registration error. For this purpose, three different data sets with different level of relief displacement are considered and three different strategies are proposed. In the proposed method, by dividing the image into patches, selecting the appropriate local window, and local matching in each window, an attempt has been made to obtain the proper distribution of points in the image. Also, by limiting the search space, the matching speed is also increased. To evaluate the proposed method, the comparison with the ENVI and ArcGIS software has been made where results clearly present the superiority of the proposed method by average of 0.28 pixel in accuracy.