The association between estimated glomerular filtration rate (eGFR) and the risk of diabetes remains uncertain. We aimed to examine the association between eGFR based on creatinine (eGFRcr), cystatin C (eGFRcys), or a combination of both (eGFRcr-cys) and new-onset diabetes, using data from the China Health and Retirement Longitudinal Study (CHARLS), a nationally representative cohort study. A total of 4,775 participants with pertinent measurements and without diabetes at baseline from CHARLS were included in the final analysis. The eGFR was calculated by creatinine, cystatin C or a combination of both using the Chronic Kidney Disease Epidemiology Collaboration equations. The study outcome was new-onset diabetes, defined as physician-diagnosed diabetes or use of glucose-lowering drugs during follow-up, or fasting glucose ≥ 126 mg/dL, random glucose ≥ 200 mg/dL, or HbA1c ≥ 6.5% (48 mmol/mol) at the exit visit. The mean age of the study population was 59.6 years. The mean values for the eGFRcr, eGFRcys, and eGFRcr-cys were 92.4, 78.9 and 85.9 mL/min/1.73m2, respectively. Over 4 years of follow-up, 612 (12.8%) participants experienced diabetes. Participants with lower eGFRcr-cys (< 60 mL/min/1.73m2) had a significantly higher risk of new-onset diabetes (adjusted OR, 1.46; 95%CI: 1.02, 2.09), compared to those with eGFRcr-cys ≥ 60 mL/min/1.73m2. However, there was no significant association between eGFRcr (< 60 vs. ≥ 60 mL/min/1.73m2; adjusted OR, 1.27; 95%CI: 0.75, 2.17) or eGFRcys (adjusted OR, 1.04; 95%CI: 0.80, 1.36) and new-onset diabetes. Lower eGFRcr-cys (< 60 mL/min/1.73m2), but not eGFRcr or eGFRcys, was significantly associated with an increased risk of new-onset diabetes in Chinese adults.