Objective To compare the efficacy and safety of endoscopic submucosal resection with ligation (ESMR-L) with non-submucosal injection and endoscopic submucosal dissection (ESD) on management of rectal neuroendocrine tumor (NET). Methods The prospective study included 42 patients who had rectal NET with a diameter ≤1 cm and received endoscopic treatment in Ruijin Hospital, Shanghai Jiao Tong University School of Medicine from October 2020 through October 2021. Twenty-one patients were treated with ESD and 21 patients were treated with non-submucosal injection ESMR-L. The average operation time and histopathological characteristics, such as complete resection rate and the distance between the lower edge of the tumor and the vertical cutting edge, were compared between the two groups. Results The operation time in non-submucosal injection ESMR-L group was significantly shorter than that in ESD group[(10.10±1.37) min vs (29.90±3.81) min, P<0.001]; The lateral and vertical margins of the two groups were both negative, and patients of both group all had the lesions complete resected (P>0.05); The distance from the lower edge of tumor to the vertical cutting edge in non-submucosal injection ESMR-L group was significantly longer than that in ESD group [(1 051.5±561.4) μm vs(612.6±305.4) μm, P=0.038]. Conclusions Compared with the ESD method, non-submucosal ESMR-L method needs shorter operation time while achieving similar rate of complete lesion resection. ESMR-L is therefore a simple, safe and effective treatment for rectal NET with diameter ≤1 cm.