Objective To explore risk factors of lymph node metastasis (LNM) in T1 rectal cancer. Methods The retrospective case-control study was conducted. The clinicopathologic data of 247 patients with T1 rectal cancer underwent radical resection were analyzed in the pathological database of the West China Hospital from January 2000 to December 2016, including the tumor size (maximum diameter), gross type, differentiation degree, histological type, lymph vascular infiltration, perineural infiltration, and carcinoma nodule. The univariate analysis and multivariate analysis were done using the Chi-square test and logistic regression model, respectively. Results The rate of LNM in the patients with T1 rectal cancer was 8.50% (21/247). No lymph metastasis was found in the well differentiated T1 rectal cancer. The results of the univariate analysis showed that the differentiation degree, histological type, and carcinoma nodule were related to the LNM in the T1 rectal cancer (P<0.050). The results of the multivariate analysis revealed that the poor differentiation, mucinous adenocarcinoma, signet-ring cell carcinoma, and carcinoma nodule were the independent risk factors of the LNM in the T1 rectal cancer (OR=9.75, P=0.006; OR=5.98, P=0.042; OR=8.33, P=0.017; OR=10.87, P=0.026). Conclusion In this large population dataset, poor differentiation, mucinous adenocarcinoma, signet-ring cell carcinoma, and carcinoma nodule are risk factors of LNM in T1 rectal cancer.