Objective To investigate the association between vitamin D and chronic kidney disease (CKD) in elderly patients. Methods The clinical and follow-up data of elderly patients aged≥60 years diagnosed with CKD at stage 1-4 were collected in the Department of Nephrology and Department of Geriatrics of Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine from January 2014 to May 2019. The serum 25-hydroxy vitamin D[25(OH)D] level was detected using photochemical method. All patients were divided into vitamin D deficiency group [25(OH)D<50 nmol/L] and non-deficiency group [including sufficient and insufficient levels of 25(OH)D, namely 25(OH)D≥50 nmol/L] according to 25(OH)D level. The baseline clinical and prognostic indicators were compared between two groups. Results Totally 347 elderly CKD patients were enrolled in this study. Compared to the patients with stage 1-2 CKD, the vitamin D level in those with stage 3-4 CKD was significantly lower. The incidence of vitamin D deficiency in the patients with stage 1-2 CKD and stage 3-4 CKD was 46.7% and 67.6%, respectively. Compared with the patients without vitamin D deficiency at stage 3-4 CKD, the patients with vitamin D deficiency at same stage had higher parathyroid hormone, serum uric acid, serum creatinine and rate of estimated glomerular filtration rate(eGFR) decline of at least 30% or progression into end-stage renal disease (16.9% vs 2.9%, P=0.042), and lower serum calcium and eGFR. The multivariate Logistic regression analysis showed that the vitamin D deficiency was an independent risk factor for the patients with stage 3-4 CKD after adjusting gender, age, mean arterial pressure, hemoglobin, albumin, proteinuria, and uric acid. Conclusions The patients with vitamin D deficiency at stages 3-4 CKD had significantly lower eGFR. The vitamin D deficiency is an independent risk factor for onset of CKD at stages 3-4.