Pneumonia is one of the most serious infectious diseases for elderly people who have impaired organ functions and are more susceptible to infection. Elderly patients having pneumonia often need long-term hospitalization, leading to declined quality of life, and increase of financial burden to the society and their family. Therefore, studies on novel therapeutic strategies and the clinical prognosis of the pneumonia patients are imperative. In the present study, we found that the Chinese herbal medicine Fu Zheng decoction had great immunomodulatory effects during the recovery period of elderly pneumonia patients. Patients treated with combined treatment of Fu Zheng decoction and antibiotic had a faster decline of temperature and a more significant decrease of C reactive protein and inflammatory factors level, and it is easier for them to cough off phlegm, compared with the antibiotic only treatment. Furthermore, the inflammation absorption and the reduction of NK-cell proportion as well as the inflammatory factors were more remarkable in the patients taken Fu Zheng decoction. Especially, the Fu Zheng decoction treatment could decrease the duration of antibiotic treatment, which may help reduce the side effects of antibiotics. Our study also found that MyD88 might play a role in the immunomodulatory effect of Fu Zheng decoction. Our study provides novel insight for the further development of intravenous injection of Chinese materia medica preparation on the regulation of immune function.