Objective To explore the value of surgical treatment in rectal small cell neuroendocrine carcinoma (RSCC). Method The clinical data of patients with pathologically diagnosed as RSCC from 2000 to 2019 were extracted from the Surveillance, Epidemiology and End Results (SEER) database, to explore the effect of surgical treatment on cancer-specific survival (CSS) and overall survival (OS). Results A total of 348 cases were included with the median follow-up of 8 months (IQR: 3–16 months). Of the 101 patients in the operation group, 84 died (83.2%), including 56 tumor-related deaths (55.4%). Of the 247 patients in the non-operation group, 215 died (87.0%), including 131 tumor-related deaths (53.0%). The estimated 1-year OS of the operation group and the non-operation group were 49.6% and 34.4%, respectively, and the estimated 1-year CSS of those were 62.2% and 49.2%, respectively. There were significant differences between the two groups (both P<0.05). Results of multivariate prognostic analysis by Cox proportional hazard model showed that differentiation, SEER stage, receiving operative treatment or not, receiving chemotherapy or not, and receiving radiotherapy or not were independent influencing factors for OS, and SEER stage, receiving operative treatment or not, receiving chemotherapy or not, and receiving radiotherapy or not were independent influencing factors for CSS (all P<0.05). The OS [RR=0.61, 95%CI was (0.45, 0.81), P<0.001] and CSS [RR=0.67, 95%CI was (0.47, 0.95), P=0.025] in RSCC patients were significantly improved by surgical treatment. Conclusion Surgical treatment can improve the OS and CSS in RSCC patients.