Objective To explore the effectiveness of the formula of spleen-tonifying, stasis-dispelling, and toxins-removing under the theory of "deficiency-stasis-toxins" in the treatment of patients with chronic atrophic gastritis and its effects on the pepsinogen (PG) and inflammatory factors levels. Methods A total of 86 patients with chronic atrophic gastritis were selected as the study subjects and randomly divided into a control group or a study group, with 43 cases in each group. The control group was given conventional treatment, based on which the study group was given the formula of spleen-tonifying, stasis-dispelling, and toxins-removing under the theory of "deficiency-stasis-toxins" additionally, and both groups were treated for 8 weeks. The clinical efficacy, traditional Chinese medicine syndromes scores, and levels of PG and inflammatory factors were compared between the two groups. Results After 8 weeks of treatment, the total effective rate and levels of PGⅠ and PGⅡ in the study group were higher than those in the control group. The scores of epigastric distending pain, chest and rib pain, fatigue, and belching, as well as levels of interleukin-6, tumor necrosis factor-α, C-reactive protein, and tumor-specific growth factor, were lower than those in the control group (all P<0.05). Conclusion The formula of spleen-tonifying, stasis-dispelling, and toxins-removing under the theory of "deficiency-stasis-toxins" can effectively ameliorate the clinical symptoms, improve the damage of gastric mucosa, reduce inflammatory response, and improve the treatment effect in patients with chronic atrophic gastritis.