Currently, the detection of renal vascular lesions (VLS) in lupus nephritis (LN) mainly depends on biopsy examination, and lack surrogate biomarkers for clinical dynamic evaluation. The aim of the present study is to explore the correlation between circulatory endothelial damage biomarkers and VLS. Soluble E-selectin, thrombomodulin (TM) and vascular cell adhesion molecule-1 (VCAM-1) were measured by ELISA. TM and VCAM-1 levels both were significantly elevated in LN with VLS than in LN without VLS (P < 0.01). However, the serum E-selectin was not significantly changed in LN patients with and without VLS. A positive correlation was found between TM and serum creatinine (r = 0.617, P < 0.05) in patients with vascular lesions. In order to further analyse the relationship between TM level and severity degree of vascular lesions in LN patients, we subdivided the patients with vascular lesions into two groups: with thrombotic microangiopathy (TMA) and without TMA. TM level of the patients with TMA is significantly higher than those without TMA (P < 0.01). In conclusion, combined with renal pathological examination, monitoring the circulatory levels of TM and VCAM-1, can provide circulating biomarkers of VLS in LN patients.