Pneumonia is a major research core topic in the medical field, and clinical trials of pneumonia and respiratory tract infection have been ongoing. The purpose of this study was to investigate the clinical efficacy and safety of Shuanghuanghua granules in the treatment of pneumonia and respiratory tract infection based on NMR molecular imaging, and to lay a foundation for the development of new drugs. In this paper, 126 patients were randomly divided into the control group, the treatment group 1, the and treatment group 2, and were given Fengreganmao granules, Shuanghuanghua granules (ultrafine preparation), and Shuanghuanghua granules (extract preparation), respectively. The main symptom scores, sign scores, antipyretic time, and virus content before and after treatment were recorded. Statistical analysis was carried out on this basis. The experiment showed that the body temperature of the subjects in the three groups before treatment was: control group (37.59 ± 0.78), treatment group 1 (37.8 ± 0.81), and treatment group 2 (37.6 ± 0.76). After treatment, the body temperature of subjects in the three groups was: control group (36.67 ± 0.71), treatment group 1 (36.49 ± 0.43), and treatment group 2 (36.19 ± 0.25). Experiments show that Shuanghuanghua granules can significantly reduce the nasal virus, adenovirus, parainfluenza virus, etc. in the patient’s body. And it can shorten the antipyretic time of patients and has good clinical application. In addition, this study gave full play to the role of MRI molecular imaging and provided ideas and references for the clinical treatment of pneumonia and respiratory tract infection.