Objective In order to improve the standing on the studies of Exercise Prescription (EP), a systematic review was conducted to provide reference and theory for further studies. Methods A broad computerized literature search of Medlin via Ovid, PubMed in all fields, Sport Discus, CINAHL, CAM, EMbase, EBM Cochrane Database of SR, and Web of Science was carried out till June 2008. Firstly, four categorical searches were conducted with the following keywords for searches: Exercise Prescription, Physical Fitness, Exercise Therapy, Fitness Assessment, Exercise Test and RCTs, and the searched results were checked by reviewers and duplicate results were removed. Then all titles were manually searched for potential inclusion in the review. Articles retrieved, review articles were examined for further relevant references. Results There were 318 relevant articles, however, the RCTs were only 7, and systematic review and meta-analysis were only one, respectively. Considering the importance and reference values there were 93 articles were included. 1970s was the developing age of EP; 1980s more specific EP were provided for many purposes; 1990s with the techniques developing of physical fitness, exercise therapy, fitness assessment and exercise test, EP for treating and rehabilitating more chronics and civilizing diseases were developed; 2000s the RCTs and CCTs were applied in the EP studies. Conclusions The developing of EP has close relationship with the developing of physical fitness, exercise therapy, fitness assessment, and exercise test. Although the RCTs researches in this field were limited, most of them were positive to support the advantage of EP. How to highly improve the advantages and greatly decrease the risk of EP is still valuable to study in the future.