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Abstract: Objective: To investigate the influence of molecular imprinting phenomena of traditional Chinese medicines (TCMs) on basic theories of TCMs according to current situations of molecular imprinting technology and experimental studies. Method: Fundamental principles of molecular imprinting theory were followed to analyze the material basis for TCM molecules to generate the imprinting phenomena, in order to find other material basis with more direct efficacy in line with the requirements of basic theories and modernization of TCMs. Result: Compared with single-component structures, TCMs and their compound components could create super-molecular compounds through complexation, composition, chelation, inclusion, neutralization, self-assembly and chemical reaction. The material basis of TCMs was super-molecular compounds including single ingredients, and there was an inter-molecule imprinting phenomenon. Therefore, special attention should be paid to inter-super-molecule imprinting actions in studies on TCM property, quality control, processing, drug preparation and pharmacology. The compatibility of TCM compounds could significantly change the action. Conclusion: The material basis of TCMs is super-molecular compounds based on single molecular groups. Super-molecules and molecular groups act rules, which is another difference between TCM compounds and single molecular drugs.