Chronic atrophic gastritis (CAG) is a precancerous form of gastric cancer. However, with pathological diagnosis as the gold standard, the sensitivity of endoscopic diagnosis of atrophy is only 42%. We developed a deep learning (DL)-based real-time video monitoring diagnostic model for endoscopic CAG and conducted a prospective cohort study to verify whether this diagnostic model could improve the diagnosis rate of endoscopic CAG compared with that of endoscopists.A U-NET network was used to build a real-time video monitoring diagnostic model for endoscopic CAG based on DL. We enrolled 431 patients who underwent gastroscopy from October 1, 2020, to December 1, 2020. To keep the baseline data of enrolled patient uniform and control for confounding factors, we applied a paired design and included the same patients in both the DL and the endoscopist group.The DL model improved the diagnosis rate of endoscopic CAG compared with that of endoscopists. Compared with diagnoses by endoscopists, the proportions of moderate and severe CAG in the atrophy patients diagnosed by the DL model were significantly larger, the proportion of "type O" CAG was significantly larger, the number of atrophy sites found was significantly increased, and the number of biopsies was significantly decreased. Compared with diagnoses by endoscopists, in the atrophic lesions diagnosed by the DL model, the proportions of severe atrophy and severe intestinal metaplasia were significantly increased.Our study suggested the DL model could improve the diagnosis rate of endoscopic CAG compared with that of endoscopists.ChiCTR2100044458, 18/03/2020.© 2022. The Author(s).