Objective: To explore the survival difference of patients with colon and rectal neuroendocrine neoplasm (NEN) at different stages. Methods: We identified 8 679 patients with colorectal NEN diagnosed between 1988 and 2014 from the Surveillance, Epidemiology, and End Results (SEER) registry, including 5 437 rectal NEN and 3 242 colon NEN ( 1 681 cecum NEN ). Survival curve was drawn by Kaplan-Meier method. Prognostic factors were analyzed by univariate analysis and multivariate Cox regression model. Results: The ratio of male patients with colon and rectal NEN was similar to female (P=0.095). Rectal NEN patients were younger (P<0.001), more highly differentiated (P<0.001), and with earlier stage (P<0.001). Survival analysis showed that the survival of rectal NEN was superior to that of colon NEN, with 10-year tumor-specific survival rates of 86.8% and 44.8% respectively (P<0.001). Multivariate Cox analysis showed that age, gender, marital status, primary tumor site, grade, stage and surgery were independent prognostic factors of colorectal NEN (all P<0.01). The most important factor was stage (HR=3.531), followed by differentiation grade (HR=1.856). Stratified analysis displayed that the survival of rectal NEN in stage Ⅰ, Ⅱ and Ⅳ were better than those of corresponding stage of colon NEN (all P<0.05), but worse in stage Ⅲ (P=0.012). While the survival of rectal NEN were significantly better than those of colon NEN within all stages after excluding 1681 cases of cecal NEN (all P<0.05). Among the patients with well-differentiated NEN, the survival of rectal NEN in stage Ⅰ, Ⅲ and Ⅳ were better than those of corresponding stage of colon NEN (all P<0.05) while there was no significant difference in stage Ⅱ(P=0.169). For poor-differentiated NEN, only the survival of rectal NEN patients in stage Ⅳ (P=0.001) was significant longer than those of colon NEN, while there was no significant difference in stage Ⅰ, Ⅱ and Ⅲ (stage Ⅰ: P=0.760; stage Ⅱ: P=0.181; stage Ⅲ: P=0.313). Conclusions The survival of NEN patients in colon and rectum is different. Cecum NEN should be considered as a separated tumor for prognostic analysis due to its special clinicopathologic characteristics.