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Background It is inconclusive whether R1 margin determined by postoperative pathological examination indicates worse long-term survival in gastric cancer (GC) patients after curative intent resection (CIR). Hence, we aimed to systematically pool the conflicting evidence to fill this gap. Methods The present study was performed according to the published protocol and Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. Published studies examining the impact of microscopic margin status on overall survival (OS) and 5-year OS rate in GC were systematically searched in PubMed, Embase, and Cochrane Library databases. RevMan 5.3 was used to conduct statistical analysis, and the Grading of Recommendations, Assessment, Development, and Evaluations approach was used to assess the certainty of evidence for each outcome. Results Twenty-three retrospective cohort studies including 19 992 patients were analyzed. The pooled hazard ratio for OS of 14 studies was 2.06 (95% confidence interval [CI]: 1.61–2.65, low certainty), indicating that R1 margin predicted inferior OS. Subgroup and sensitivity analyses upheld the statistical stability of this finding. The pooled odds ratio (OR) of 14 studies was .21 (95% CI: .17–.26, moderate certainty), demonstrating that the presence of R1 margins was associated with a poorer 5-year OS rate. Sensitivity analyses and most of the subgroup analyses confirmed this finding, except the “esophagogastric junction (EGJ) cancers” subgroup, which included two studies with a pooled OR of .41 (95% CI: .10–1.61). Conclusion R1 margin detected by pathological examination might exhibit a high correlation with poorer OS and 5-year OS rate in GC (except EGJ cancers) patients who underwent CIR. To figure out the effect of R1 margin on survival of different stages and histological types need prospective studies with large sample sizes and standardized methods. What is the best treatment for R1 margin patients also need more in-depth and special research.