Objective To systematically evaluate the clinical efficacy and safety of Chaihu Shugan San in the treatment of chronic atrophic gastritis(CAG). Methods Electronic computer search Pubmed, Web of Science, Cochrane Library, CNKI, VIP and Wanfang database, all randomized controlled trials(RCTs) of Chaihu Shugan san for the treatment of chronic atrophic gastritis with liver-stomach disharmony were included. The search time is established for the database until October 1, 2019. And Meta analysis was performed using RevMan 5.3 software. Results A total of 1 068 patients were included in 11 studies. The results of Meta analysis showed that compared with conventional western medicine, Chaihu Shugansan san effectively improve the total clinical effective rate[RR=1.25，95%CI(1.19, 1.33), P<0.000 01], the total effective rate of symptomatic effect [RR=1.57， 95%CI(1.30， 1.89， P<0.000 01] and the serum gastrin G17 level[MD=3.61, 95%CI(2.89, 4.33), P<0.000 01] in patients with liver-stomach disharmony atrophic gastritis. And it can improve the pathological examination scores of gastric mucosal atrophy[MD=-1.53, 95%CI(-1.93, -1.12), P<0.000 01], intestinal metaplasia[MD=-0.79, 95%CI(-0.96, -0.63), P<0.000 01] and abnormal hyperplasia[MD=-0.69, 95%CI(-0.84, -0.55), P<0.000 01]. The difference in curative effect between the two groups is statistically significant. Conclusion The efficacy of Chaihu Shugan san in the treatment of chronic atrophic gastritis with liver-stomach disharmony is better than that of conventional western medicine.