With the transformation of modern medicinal pattern, medical studies are confronted with methodological challenges. By analyzing two methodologies existing in the study of physical matter system and information system, the article points out that traditional Chinese medicine (TCM), especially the treatment based on syndrome differentiation, embodies information conception of methodological positions, while western medicine represents matter conception of methodological positions. It proposes a new way of thinking about combination of TCM and western medicine by combinating two kinds of methodological methods.