The aim of this systematic review was to investigate the association between the different factors of loading protocols and the long-term stability of micro-screws from biomechanical and histological viewpoints. Searches were performed on PubMed, Embase, Cochrane Library, Wanfang and CNKI databases for animal experiments comparing loading protocols and the long-term stability of micro-screws. Among 1011 detected papers, 16 studies met the eligibility criteria and were selected for analysis. Most studies showed medium methodological quality for evaluation of micro-screws' long-term stability. Five studies reported that loading would not destroy the long-term stability of micro-screws. Three studies indicated that low-intensity immediate loading or a 3-week minimal healing time was acceptable. Two studies reported that the loading magnitude was a controversial issue with regard to the micro-screws' long-term stability. Two studies suggested that counterclockwise loading could decrease the long-term stability of micro-screws. In conclusion, immediate loading below 100g force, healing time greater than 3 weeks, regular loading below 200g force and a clockwise direction of force supported the long-term stability of micro-screws. Further studies relating to the combination of varying loading conditions will be needed.