Objective The efficacy and safety of rectal instillation with formula for clearing heat, eliminating phlegm and relaxing bowel on treating encephalopathy complicated with pulmonary infection were evaluated by randomized controlled clinical trials. Methods Eighty eligible cases of encephalopathy complicated with pulmonary infection were randomly divided into treatment group and control group. Control group was given conventional treatment and treatment group was given rectal instillation treatment with formula for clearing heat , eliminating phlegm and relaxing bowel. The changes of index were observed before and after treatment in two groups including temperature,antifebrile time,white blood cell count,neutrophils ratio,C-reactive protein,procalcitonin, pneumonia severity index,and the efficacy score of TCM syndrome. Results Rectal instillation with formula for clearing heat and eliminating phlegm to relax bowel can be better improved encephalopathy complicated with pulmonary infection with syndrome of phlegm-heat obstructing in which the patients have yellow sputum, constipation,yellow urinary and other symptoms. It can reduce TCM syndrome score and level of serum calcitonin, relieve inflammation,enhanc antibacterial effect,and improve the clinical curative effect. Conclusions The curative effects of rectal instillation with formula for clearing heat and eliminating phlegm to relax bowel on treating encephalopathy complicated with pulmonary is definite which has no adverse reaction and safety use. It is worthy of further popularizing in clinic.