Objective Based on the syndrome differentiation of traditional Chinese medicine, the microscopic indexes such as the changes of mucosa and histopathology under gastroscope were applied to the syndrome differentiation analysis to find the relationship between the microscopic indexes and the syndrome types of chronic atrophic gastritis. Methods 190 patients with chronic atrophic gastritis were selected from the outpatient department of Guang′anmen Hospital, Chinese Academy of traditional Chinese medicine from January 1, 2021 to December 31, 2021. According to the consensus on TCM diagnosis and treatment of chronic atrophic gastritis in 2010, the TCM Syndrome Types and gastroscopic gastric mucosal signs, TCM Syndrome Types and Kimura bamboo classification, TCM Syndrome Types and histopathological changes were analyzed. Results Logistic regression analysis of TCM Syndrome Types and gastric mucosal signs under gastroscope showed that there was a positive correlation between gastric collateral stasis syndrome and gastric mucosal white phase (P<0.05). It can be concluded that the syndrome of disharmony between liver and stomach is positively correlated with the thinning of gastric mucosa(P<0.05), the syndrome of damp heat of spleen and stomach is positively correlated with the edema of gastric mucosa(P<0.05), and the syndrome of weakness of spleen and stomach is positively correlated with the bleeding of gastric mucosa(P<0.05). Logistic regression analysis of TCM Syndrome Types and gastric mucosal signs under gastroscope showed that there was a correlation between stomach collateral stasis syndrome and Kimura bamboo classification(P<0.05). Patients with stomach collateral stasis syndrome had a higher probability of Kimura bamboo classification as closed type than patients with non stomach collateral stasis syndrome. To analyze the correlation between TCM syndrome types and histopathological changes showed thatthe liver stomach disharmony syndrome was correlated with OLGA and OLGIM. Conclusion The study found that there is a certain correlation between the TCM syndrome types and the endoscopic mucosal image changes, atrophic range and histopathological changes of chronic atrophic gastritis.