Background. The performance of various equations for estimated glomerular filtration rate (eGFR) in patients with diabetes remains controversial. We aimed to evaluate the performance of equations for eGFR in Chinese patients with diabetic nephropathy (DN). Methods. This is a retrospective study included in 308 patients with type 2 diabetes and biopsy-proven DN who were followed up at least one year. eGFR was calculated using chronic kidney disease epidemiology (CKD-EPI) equations based on serum creatinine (eGFRCKD-EPI-Cr), cystatin C (eGFRCKD-EPI-CysC), and joint equations (eGFRCKD-EPI-Cr-CysC), respectively. End-stage kidney disease was defined by initiation of renal replacement therapy. The eGFR concordance between equations was assessed by Bland-Altman plots. Log-rank and multivariable logistic regression were employed to evaluate the performance of equations. Results. Overall, the proportion of patients with eGFR<60 mL/min/1.73m2 was 53%, 70%, and 61% by the equations of eGFRCKD-EPI-Cr, eGFRCKD-EPI-CysC, and eGFRCKD-EPI-Cr-CysC, respectively. Higher disconcordance was observed between equations when eGFR>60 mL/min/1.73m2. Compared with eGFRCKD-EPI-Cr, 39% of patients were reclassified (reclassified group) from CKD 1-2 stages to CKD 3-5 stages by eGFRCKD-EPI-CysC and they presented significantly longer diabetic duration, heavier proteinuria, advanced pathological lesions, and poorer kidney outcomes. Multivariable logistic regression indicated cystatin C was independently associated with advanced glomerular classifications. Conclusion. eGFR equations incorporating cystatin C are superior to eGFR based on creatinine alone for detecting kidney injury in the early stage. The independent association between cystatin C and glomerular classifications might contribute to it.