In recent years, the ancient Yin-Yang theory has been gradually adopted by modern researchers, especially European and American scholars, and it has also been applied to modern scientific research on sleep, viruses, metabolism, cancer, genes, autoimmune diseases, and so on. It is very promising and fruitful results have been reported. However, the understanding of the connotations of Yin-Yang theory is not sufficient and thorough enough in these studies. If we understand and apply Yin-Yang theory more comprehensively, it may provide us with additional potential mechanisms and research directions worthy of study. On the basis of promoting a comprehensive understanding of all three connotations of Yin-Yang theory, this review attempts to illustrate this theory, summarize its applications in modern scientific research, and reveal the potential research direction of modern medicine.