Abstract: This paper is to reveal the application laws and value of Yunqi theory in the prevention and treatment of pestilence and to discover the thoughts and methods of the ancient Chinese medicine doctors in the prevention and treatment of pestilence by applying Yunqi theory. This paper explains the scientificalness of pestilence Yunqi theory which is based on the holism of heaven， earth and human， and analyzes the basic types of pestilence and typical formula. It is considered that the modern research orientation of the prevention and treatment of pestilence by applying Yunqi theory is: the Yunqi theory and laws of the pestilence occurence from the perspective of astrometeorology-time-geography-space-time medicine.