Objective To evaluate the new scoring system for gastric cancer screening and risk assessment of gastric precancerous lesions. Methods A total of 442 patients who underwent endoscopy due to stomach discomfort at the First Hospital of Jiaxing from March 2018 to September 2019 were enrolled. The patients were divided into three groups based on the new scoring system for gastric cancer screening before endoscopy: low-risk group (0-11 points), median-risk group (12-16 points) and high-risk group (17-23 points). The detection rates of gastric cancer and atrophic gastritis in three groups were analyzed. According to the range or degree of atrophy or intestinal metaplasia, patients were divided into five groups of stage 0 to Ⅳ based on the operative link for gastritis assessment (OLGA) or operative link for gastritis intestinal metaplasia (OLGIM). The correlation between the new gastric cancer screening scoring system and OLGA or OLGIM staging system were evaluated. Results Among 442 patients, 211 were assigned to low-risk group, 207 median-risk group and 24 high-risk group according to the new scoring system. For OLGA staging system, there were 241 cases of stage-0, 105 of stage-Ⅰ, 58 stage-Ⅱ, 27 stage-Ⅲ and 11 stage-Ⅳ. For OLGIM staging system, there were 224 cases of stage-0, 113 stage-Ⅰ, 61 stage-Ⅱ, 31 stage-Ⅲ and 13 stage-Ⅳ. The pepsinogen (PG) Ⅰ and pepsinogen ratio (PGR) levels had differences among different OLGA stages (F=2.844, P＝0.027; F=5.435, P＝0.001), and these two variables at Stage-Ⅲ and Ⅳ were significantly lower than three other OLGA stages (all P<0.001). The PGR level had differences among different OLGIM stages (F=3.887, P＝0.008), which was significantly lower at Stage-Ⅳ than at other OLGIM stages (all P<0.001). Gamma coefficient analysis and Kendall""s tau-b analysis showed significant correlations between OLGA/OLGIM staging system and new gastric cancer screening scoring system (P<0.001). Conclusion The new scoring system is reliable for gastric cancer screening, and is closely linked with OLGA/OLGIM staging system in the risk assessment of gastric precancerous lesions.