To conduct a meta-analysis to provide accurate evidence regarding the preferred diagnostic method, magnifying endoscopy (ME) or endoscopic ultrasonography (EUS), for assessment of the depth of invasion of the gastrointestinal neoplasms. PubMed, EMBASE, Ovid Medline, and the Cochrane Library databases were searched for studies published between January 1946 and October 2016, regarding the use of EUS and ME to assess the invasion depth of gastrointestinal cancers. The quality of diagnostic studies was evaluated using the QUADAS2 instrument. The Meta-DiSc software (version 1.4) was used for meta-analysis of the pooled data regarding the diagnostic accuracy of EUS and ME of the invasion depth of gastrointestinal neoplasms. Our meta-analysis included the data of 754 patients with gastrointestinal cancers contributed by seven prospective studies. All studies were of high quality (QUADAS2). The receiver operating characteristic (ROC) planes were not observed in shoulder and arm forms for either EUS or ME, with Spearman's correlation coefficients of -0.821 and 0.234 for EUS and ME, respectively. The p values of the diagnostic odds ratio for EUS and ME were 0.0038 and 0.0131, respectively. The sensitivity and specificity of EUS for the diagnosis of the depth of invasion of gastrointestinal cancers were 0.75 (95% CI 0.69-0.81) and 0.84 (95% CI 0.79-0.88), respectively. In comparison, the sensitivity and specificity for ME were 0.74 (95% CI 0.67-0.69) and 0.85 (95% CI 0.80-0.89), respectively. The values of area under the summary ROC (SROC) curves for EUS and ME were 0.8499 and 0.8757, respectively, with a non-significant Z value between EUS and MR (0.296 < 1.96). Both EUS and ME provide a comparable performance for judging the depth of invasion of gastrointestinal neoplasms. However, there is heterogeneity between studies contributed by non-threshold effects.