Qi deficiency in the spleen and stomach is considered to be the fundamental pathogenesis of chronic atrophic gastritis (CAG) in Traditional Chinese medicine. Spleen strengthening and Qi replenishment are the basic treatment principles. Sijunzi Decoction serves as the fundamental remedy for spleen notification and Qi replenishment. The Cochrane Library, China National Knowledge Infrastructure China Biology Medicine disc, VIP, Wanfang Database, Web of Science, PubMed, and Embase were retrieved for related randomized controlled trials published from the inception of the databases to June 3, 2023. Literature screening and data extraction were executed by 2 independent investigators. The Cochrane Collaboration tool was leveraged to appraise the quality of included studies. Meta-analysis was implemented utilizing Stata 15. This analysis incorporated 32 studies with 2780 patients. The analysis results unveiled that compared to Western medicine treatment, modified Sijunzi Decoction significantly enhanced the clinical efficacy (relative risk [RR] = 1.241, 95% confidence interval [95% CI] = 1.199-1.285, P < .0001), lowered symptom scores (standardized mean difference [SMD] = -1.846, 95% CI = -2.160 to -1.532, P < .00001) and gastroscopic pathological scores (SMD = -1.122, 95% CI = -1.492 to -0.752, P < .00001), ameliorated quality of life (SMD = 4.294, 95% CI = 2.982-5.606, P < .00001), increased the Helicobacter pylori eradication rate (RR = 1.297, 95% CI = 1.035-1.625, P < .001), pepsinogen I levels (SMD = 2.615, 95% CI = 2.344-2.886, P < .00001), pepsinogen I/II ratio (SMD = 3.107, 95% CI = 2.811-3.403, P < .00001), and gastrin-17 levels (SMD = 1.004, 95% CI = 0.794-1.215, P < .00001), and reduced the incidence of adverse reactions (RR = 0.361, 95% CI = 0.235-0.556, P < .01) in individuals with CAG, with statistically significant discrepancies. Modified Sijunzi Decoction exhibited superior efficacy to conventional Western medicine in treating CAG. It was shown to improve the Helicobacter pylori eradication rate, reduce symptom scores, enhance quality of life, and improve pepsinogen-related indicators with a high safety profile.