Background. Nanotargeted preparations can enhance the safety and effectiveness of medication by altering the pharmacokinetic behavior of drugs in the human body, and Pueraria lobata is shown to be effective in the treatment of neck and back pain. Purpose. This study prepared a nano-Pueraria targeted preparation, in order to analyze its effect on improving the clinical symptoms of cervical spondylosis by adjusting the balance of intestinal flora. Methods. A total of 200 patients with cervical spondylosis admitted to the Affiliated Hospital of Nanjing University of Chinese Medicine were enrolled and divided into an observation group and a control group. The control group was given Tuina therapy, and the observation group was given nano-Pueraria targeted preparation + Tuina therapy. The clinical symptoms and intestinal microflora of the two groups were examined before intervention. Results. It was found that the markedly effective of treatment efficacy of the observation group (98%) was higher than that of the control group (78%) after 15 days of intervention, and the clinical symptoms were obviously fewer than those of the control group. The distribution of gut microbiota showed that there were significant differences in the composition of gut microbiota between the two groups. Compared with the control group, the abundance of Firmicutes in the observation group was significantly higher, while the abundance of Bacteroidetes and Proteobacteria was significantly lower. Conclusion. The targeted preparation of nano-Pueraria can improve the clinical symptoms of patients with cervical spondylosis by adjusting the balance of gut microbiota.