Stressing the uniqueness and complexity of traditional Chinese medicine (TCM) theory system, this paper analyzes the characteristics of TCM as a discipline from four perspectives: scientific nature, fundamental theory, clinical practice, and pharmacological action. It suggests that when the research strategy of TCM theory is designed, the core theory of TCM should be emphasized on the theoretical research on TCM original thinking theory, TCM theory, Chinese materia medica and formulas, acupuncture and moxibustion, meridians and collaterals, and other related fields. Researchers and practitioners should ensure that the basic research on TCM theory is based on clinical practice, research methods (both traditional and contemporary) are exploited, and methodological innovation is underscored. The rule of TCM development should be followed and the characteristics and advantages of TCM carried forward. Meanwhile, the methods and theory of contemporary science and technology should be exploited to fulfill the goal of inheriting, enriching, and developing the fundamental theory of TCM.