Abstract: The clinical trial protocol is the core of clinical trial, indispensable to the scientificity, reliability and accuracy of clinical trial results. In the early stage of emerging infectious diseases, the design of clinical trial protocol is unique due to the urgency of clinical diagnosis and treatment, the necessity of clinical research, the inadequacy of disease knowledge, the particularity of research environment, the possible changes of social environment and the inadaptability of research team. We considered the actual early epidemic situation, and analyzed several key contents in design and implementation of clinical trial protocol, in order to provide reference for the design of clinical trial protocol.

Key words: emerging infectious diseases ,  clinical research ,  clinical trial protocol ,  intervention research