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The mode of scientific thinking is undergoing rapid and profound changes. In the 21st century, macro and micro civilizations go parallel. A systematic and scientific methodology is required for the study of complex things. The thinking mode in modern medicine is gradually shifting from analytical, reductive thinking to holistic and systematic thinking. As such Western medicine and traditional Chinese medicine are gradually approaching the epistemology of health and disease state. The importance of scientific thinking in innovation has been expounded in this study. The development trends in medicine in the current era are analyzed, the importance of systems theory in the study of human bodies is discussed, and a new medical model named Novel Systems Medicine is proposed.