BackgroundSize and number of lymph nodes (LNs) were reported to be associated with the prognosis of stage II colorectal cancer (CRC). The purpose of this study was to determine the prognostic role of the size of LNs (SLNs) measured by computer tomography (CT) and the number of retrieved LNs (NLNs) in the relapse-free survival (RFS) and overall survival (OS) among stage II CRC patients.MethodsConsecutive patients diagnosed with stage II CRC at Fudan University Shanghai Cancer Center (FUSCC) from January 2011 to December 2015 were reviewed, and 351 patients were randomly divided into two cohorts for cross-validation. The optimal cut-off values were obtained using X-tile program. Kaplan-Meier curves and Cox regression analyses were conducted for the two cohorts.ResultsData from 351 stage II CRC patients were analyzed. The cut-off values for SLNs and NLNs were 5.8 mm and 22, respectively, determined by the X-tile in the training cohort. In the validation cohort, Kaplan-Meier curves demonstrated SLNs (P = 0.0034) and NLNs (P = 0.0451) were positively correlated with RFS but not with OS. The median follow-up time in the training cohort and the validation cohort were 60.8 months and 61.0 months respectively. Univariate and multivariate analysis revealed that both SLNs (training cohort: Hazard Ratio (HR) = 2.361, 95% Confidence interval (CI): 1.044–5.338, P = 0.039; validation cohort: HR = 2.979, 95%CI: 1.435–5.184, P = 0.003) and NLNs (training cohort: HR = 0.335, 95%CI: 0.113–0.994, P = 0.049; validation cohort: HR = 0.375, 95%CI: 0.156-0.900, P = 0.021) were independent prognostic factors for RFS whereas not for OS.ConclusionSLNs and NLNs are independent prognostic factors for patients with stage II CRC. Patients with SLNs > 5.8 mm and NLNs ≤ 22 are apt to have higher risk of recurrence.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12885-023-10935-x.