Abstract：Fuxie Xinshu (New Treatise on Hidden Pathogens) put forward for the first time that "lingering pathogen hidden internally"， which was attributed to one of the hidden pathogen， and was explained as eliminating the clinical symptoms， but failed to eliminate the root cause of the disease， causing the remnant pathogen to lurk in the body and wait for an opportunity to attack. The internal remnant pathogen can cause external and internal injuries， while different schools have different views on the potential location of pathogenic qi. The legacy of pathogenic qi can cause disease recurrence，disease lingering and difficult to heal. Before recurrence，the disease is often mild and difficult to recognize，so common clinical patients have no obvious discomfort，but they should also consult the medical history，comprehensively collect the four diagnostic data，and grasp the pathogenesis before the occurrence of the disease. From the perspective of modern medicine，we can also understand the theory of endogenous pathogens from the clinical mechanism of disease recurrence， such as small residual focus， tumor cell niche， circulating tumor cells， and infectious diseases virus. Comprehensive analysis of clinical treatment methods for the hidden pathogen， on the basis of syndrome differentiation and treatment， when strengthening the righteousness and eliminating pathogenic factors are parallel， strengthening the righteousness lies in regulating and replenishing the zang fu organs， and eliminating pathogenic factors emphasizes giving the pathogen a way out and guiding it according to the situation. From the aspect of patients themselves，they should follow the Huangdi Neijing (The Yellow Emperors's Internal Classic) to nourish their health. They should eat and drink properly， live a regular life， do not overwork， avoid pathogenic qi externally， and nourish their spirit inside.