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Terraces are the major land-use type of agriculture and support the main agricultural production in southeast and southwest China. However, due to smallholder farming, complex terrains, natural disasters and illegal land occupations, a light-weight and low cost dynamic monitoring of agricultural terraces has become a serious concern for smallholder production systems in the above area. In this work, we propose a small unmanned aerial vehicle (UAV) based multi-temporal image registration method that plays an important role in transforming multi-temporal images into one coordinate system and determines the effectiveness of the subsequent change detection for dynamic agricultural terrace monitoring. The proposed method consists of four steps: (i) guided image filtering based agricultural terrace image preprocessing, (ii) texture and geometric structure features extraction and combination, (iii) multi-feature guided point set registration, and (iv) feature points based image registration. We evaluated the performance of the proposed method by 20 pairs of aerial images captured from Longji and Yunhe terraces, China using a small UAV (the DJI Phantom 4 Pro), and also compared against four state-of-the-art methods where our method shows the best alignments in most cases.