Abstract Background Multiple primary esophageal squamous cell carcinoma (MPESCC) is a rare and complex type of esophageal cancer, categorized into synchronous multiple primary esophageal squamous cell carcinoma (S-MPESCC) and metachronous multiple primary esophageal squamous cell carcinoma (M-MPESCC). Compared to solitary esophageal squamous cell carcinoma (SESCC), multiple primary esophageal squamous cell carcinoma (MPESCC) generally has a poorer prognosis, with significant differences in treatment strategies and survival outcomes. This study aims to explore the clinical characteristics and prognosis of S-MPESCC through a retrospective analysis of a large patient cohort. Methods This study retrospectively analyzed clinical data from 758 patients with esophageal squamous cell carcinoma (ESCC) who underwent surgical resection at two medical centers in China from January 2012 to December 2021. The S-MPESCC group included 68 patients, and the SESCC group included 690 patients. All patients underwent radical esophagectomy with systematic lymph node dissection. Preoperative and postoperative data were collected, including gender, age, family history, tumor staging, and lymph node metastasis. Results There were no significant differences in baseline characteristics, such as gender, age, and family history, between the S-MPESCC and SESCC groups. The lymph node metastasis rate was significantly higher in the S-MPESCC group compared to the SESCC group, especially in the upper mediastinal and abdominal regions (P<0.05). Survival status was monitored through outpatient visits and telephone calls until December 2022. The results showed that the 3-year and 5-year survival rates of the S-MPESCC group were significantly lower than those of the SESCC group (P< 0.05). Patients with a greater depth of primary tumor infiltration had poorer survival outcomes in the S-MPESCC group. Conclusion This study clarified the clinical characteristics and prognosis of S-MPESCC through a retrospective analysis of 758 ESCC patients. S-MPESCC patients had a significantly higher rate of lymph node metastasis and a poorer prognosis compared to SESCC patients. Future efforts should focus on optimizing treatment strategies to improve the prognosis and survival rates of patients with S-MPESCC.