With the help of missionaries, western medicine had entered into China in the past 100 years. The inherent difference between Chinese traditional medicine and western medicine caused widespread disputes in scientific circles, medical arena, the philosophy and the political. Therefore, Chinese traditional medicine fell into the mess of survival and development several times. However, men’s development couldn’t depart from any kinds of cultural and any kinds of knowledge. The simple discuss on either retention or abandonment of Chinese traditional medicine seemed too extreme. Facing contradiction and the difference of Chinese and western medicine,we should start from the source,analyze the disagreement from historical vein, scan the region, the humanities environment, the thought and the language that affected the medical development,then understand and eliminate the difference, and realize the Chinese traditional medicine and the western medicine perfect union.