Abstract: Based on special scientific facts demonstrated in traditional Chinese medicine (TCM) complex system, this paper proposes a hypothesis of "one output multi-source", discussing the concept, features, structures and the scope. The law of interaction between the integrity and multiple components of TCM complex system was examined. Feasibility, technical methods and evidence supporting the hypothesis have been presented here. We present a basic model of the hypothesis, i.e. artificial neural network (ANN) model. This hypothesis promotes a deeper modern scientific understanding towards the TCM complex system and advancement in research of the material basis. TCM compatibility and quality control will serve as the theoretical foundation for guiding the research on drug combination including chemical, biological and herbal medicines.