BACKGROUND Ampullary cancer is a relatively rare malignant tumor in the digestive system. Its incidence has increased in recent years. As for now, its biological characteristics have not been fully clarified. Recent studies have primarily focused on the histological classification and genetic changes, but there are fewer investigations into the differences among site-specific subgroups. The clinicopathological characteristics of ampullary cancer occurring in different positions have not been elucidated. Furthermore, the role of adjuvant therapy in the treatment of patients with ampullary cancer remains controversial. AIM To study the clinicopathological features of the two site-specific subgroups of ampullary cancer and explore the factors affecting prognosis. METHODS A total of 356 patients who met the inclusion and exclusion criteria were enrolled. Patients were divided into ampulla of Vater cancer (AVC) and duodenal papilla cancer (DPC) based on the gross and microscopic findings. Baseline data, admission examination results, and perioperative outcomes were collected and analyzed. The Kaplan-Meier curve was used for survival analysis. Univariate and multivariate analysis was performed to explore the independent risk factors affecting the overall survival (OS) of both groups. RESULTS The preoperative total bilirubin level in patients with AVC was significantly higher than those with DPC (P = 0.04). The OS for patients with DPC was 58.90 ± 38.74 months, significantly longer than 44.31 ± 35.90 months for patients with AVC (P < 0.01). The independent risk factors affecting the OS of AVC included: Preoperative albumin level (P = 0.009), total bilirubin level (P = 0.017), and number of positive lymph nodes (P = 0.005). For DPC, risk factors included: Age (P = 0.004), tumor size (P = 0.023), number of positive lymph nodes (P = 0.010) and adjuvant treatment (P = 0.020). Adjuvant therapy significantly improved the OS rate of patients with DPC, but not for those with AVC. CONCLUSION Patients with AVC had a shorter OS compared to those with DPC. The prognosis factors and the role of adjuvant therapy of two groups were different.