Objective: We sought to investigate clinicopathological characteristics correlated with the prognosis of uveal melanoma (UM) patients and find the driving factors of prognosis for ciliary/iris melanoma relative to choroid melanoma. Materials and Methods: We collected patients with uveal melanoma between 1983 and 2012 from the Surveillance, Epidemiology, and End Results (SEER) database. Primary outcomes were evaluated as cancer-specific survival (CSS) and overall survival (OS). The Kaplan-Meier analysis was applied for the univariate analysis of CSS and OS and corresponding survival curves. Cox proportional hazards regression was used for multivariate analysis to value hazard ratio (HR) of ciliary body/iris melanoma subgroup versus choroid melanoma subgroup. Results: A total of 4359 eligible patients were collected in our study. Novel potential prognostic factors for CSS and OS of UM were identified. Age at diagnosis, sex, primary tumor site, histologic subtype, tumor size, the extent of disease, and treatment were the independent prognostic factors for UM patients (P < 0.05). Interestingly, when concerned with the primary site of UM, we found that the ciliary body/iris melanoma subgroup showed significant differences in prognosis (both CSS and OS), sex, histologic type, the extent of disease, and treatment options relative to choroid melanoma subgroup (P < 0.05). Subsequently, stratification analyses suggested that the distinct survival outcomes between the ciliary body/iris melanoma and choroid melanoma subgroups mainly attributed to patient sex, age, tumor size, the extent of disease, and treatment options (P < 0.05). Conclusion: Age, sex, primary tumor site, histologic subtype, tumor size, the extent of disease, and treatment options are independent prognostic indicators for UM patients. Besides, the ciliary body/iris melanoma subgroup shows worse survival outcomes than choroid melanoma. Our findings offer inspiration to the individual treatment for UM patients with different primary sites.