Objective To investigate the characteristics of endoscopic ultrasonography for rectal neuroendocrine neoplasms (R-NENs) of different origin and its influence on the diagnosis and treatment. Methods A retrospective cross-sectional study was conducted to analyze 56 cases of R-NENs diagnosed by miniprobe endoscopic ultrasonography (MEUS) and/or pathology in the Endoscopy Center of Beijing Chaoyang Hospital, Capital Medical University from January 2016 to July 2021. The endoscopic ultrasonography characteristics, pathological features, surgical selection and the follow-up of R-NENs originating from deep mucosa and submucosa were compared. Results Among the 56 patients, 49 were diagnosed as R-NENs.The diagnostic sensitivity, positive predictive value and diagnostic accuracy of MEUS for R-NENs were 93.88% (46/49), 86.79% (46/53) and 82.14% (46/56), respectively. R-NENs were mainly manifested by medium hypoechoic with MEUS [95.92% (47/49)]. Three R-NENs originated from submucosa were missed diagnosis, with 1 case presenting hypoechoic and 2 cases presenting hyperechoic. There were no significant differences in the tumor diameter, echo intensity under endoscopic ultrasonography, echo uniformity and pathological grade composition between deep mucosal origin and submucosal origin R-NENS (all P>0.05), but there was significant differences in the distance from tumor to anus (χ2=5.011, P=0.025). The proportion of the distance from tumor to anus ≤5 cm of submucosal origin lesions was significantly higher than that of deep mucosal origin [43.75% (14/32) VS 17.65% (3/17)]. Endoscopic submucosal dissection [67.5% (27/40)] and transanal endoscopic microsurgery [25.0% (10/40)] were the major treatment method, but there were no significant differences in endoscopic ultrasonography manifestations and pathological grading of R-NENs between these two surgical procedures. Conclusion There is no significant difference in endoscopic ultrasonography manifestations and pathological grade of R-NENs between deep mucosal origin and submucosal origin, suggesting that the prognosis is similar between the two types. It is no significant influence of endoscopic ultrasonography manifestations of R-NENs at different levels of origin.