With the implementation of “Good Clinical Practice”, the quality of clinical trials in China has increased constantly and more importance has been attached to the protection of the subject. Large scale clinical trials are primarily featured by long-term intervention, large sample size, many participant organizations, different levels of investigators, long test periods, and lots of adverse events. Consequently, the protection of subject is full of extensive complexities and difficulties and currently there is little experience to refer to. Hence, the article introduces the subject’s protection method adopted in the National Program Subject of Secondary Prevention Clinical Trial about Effect of Qi Shen Tonifying Qi on Myocardial Infarction (MISPS-TCM).