Abstract Background Lymph node metastasis (LNM) is a crucial factor in predicting the prognosis of patients with T1–2 esophageal squamous cell carcinoma (ESCC), but the extent of lymph node (LN) dissection remains controversial. This study aims to investigate the optimal extent of LN dissection for T1–2 ESCC by analyzing the metastasis rate, evaluating the prognostic value at each LN station, and identifying risk factors for the LN stations with high LNM rate. Methods Patients with pathological T1–2 ESCC who underwent esophagectomy with LN dissection were enrolled between January 2014 and December 2019. Kaplan–Meier and Cox proportional hazards model were used to analyze the influence of LN with different metastasis rates on prognosis, respectively. The logistic regression analysis was performed to identify risk factors for the LN stations with high LNM rate. Results In total, 386 patients with T1–2 ESCC were included with a median LN dissection number of 18.5 (range: 12–48). The LN stations with LNM rate over 5% were the station 8 (11.9%), 2 (10.9%), 17 (8.0%), 16 (7.3%), and 7 (5.2%), and patients with metastasis of these stations showed significantly worse OS (P < 0.001). Moreover, the BMI (OR 0.45, 95%CI: 0.27–0.75, P < 0.01), tumor differentiation (OR 1.66, 95%CI: 1.14–2.42, P < 0.01), and T stage (OR 2.05, 95%CI: 1.21–3.47, P < 0.01) were independent risk factors of the metastasis of stations with LNM rate over 5%. Conclusions The poor prognosis of the metastasis of LN stations with LNM rate over 5% (station 8, 2, 17, 16, and 7) in T1–2 ESCC suggests the necessity of dissection, especially for patients with lower BMI, poor tumor differentiation, and deeper infiltration.