As essential concepts of the traditional Chinese medicine theory,"deficiency"and"toxin"have been enriched and developed continuously since Huangdi Neijing.By tracing back and combing"deficiency"and"toxin",this paper sums up their relationship,analyzes and explains their basic connotation,and discusses their extension.The"deficiency-toxin"theory has two meanings:it covers the pathological state of the human body with deficiency of vital qi and excess of pathogenic toxin,and it also refers to the pathological evolutionary process in which"deficiency"and"toxin"promote each other.Based on the connotation and dynamic pathogenesis of the"deficiency-toxin"theory,it is pointed out that this theory can be applied to the prevention and treatment of infectious diseases and chronic debilitating diseases,including the"inflammation-cancer transformation"of inflammatory bowel disease.Taking inflammatory bowel disease as an example and combining its Western medical background,this paper expounds on the pathogenesis and treatment of the"inflammation-cancer transformation"of inflammatory bowel disease,and provides a paradigm of"deficiency-toxin"theory guiding clinical research.