Objective To investigate the diagnostic value and influencing factors of endoscopic ultrasonography (EUS) for rectal neuroendocrine neoplasms (R-NENs). Methods A retrospective analysis was performed for 317 patients with suspected R-NENs in the Affiliated Hospital of Qingdao University from March 2016 to June 2023, and endoscopic diagnosis was obtained.Clinical data, EUS characteristics and pathological results were statistically analyzed, and the diagnostic accuracy and influencing factors of EUS for R-NENs were obtained by comparing the EUS results with the pathological results. For comparison between groups were done by the chi-square test or Fisher"s exact test, and multivariate analysis was done using the Logistic regression model. Results The sensitivity and specificity of EUS in diagnosing R-NENs were 98.03% (249/254), 34.92% (22/63), 85.86% (249/290) and 81.48% (22/27) respectively. The accuracy was 85.49% (271/317) and the Jorden index was 0.33. Tumor ultrasound diameter ≤5mm (P=0.002), normal tumor surface color (P=0.01), tumor distance > 10cm from anal margin (P=0.0070), and no dilated blood vessels on the surface of tumor (P=0.001) were independent risk factors affecting the accuracy of R-NENs diagnosis by EUS . The accuracy of EUS in diagnosing R-NENs involvement depth was 76.77% (195/254). Surface depression of tumor (p=0.035) and tumor echo heterogeneity (p < 0.001) were independent risk factors affecting the accuracy of R-NENs involvement in EUS diagnosis. Conclusions Endoscopic and ultrasonic characteristics of R-NENs are closely related to their diagnostic accuracy. EUS can not only observe the surface structure of the lesion, but also combine the characteristics of the lesion echo, origin, and depth of involvement, which not only improves the diagnostic accuracy of R-NENs, but also provides a basis for the selection of treatment methods. Therefore, EUS has a good clinical value for the diagnosis and treatment of R-NENs.