The present study was conducted to assess the association between 25-hydroxyvitamin D [25(OH)D], estimated glomerular filtration rate (eGFR) and urine microalbumin/creatinine ratio (uACR) in Korean adults. Data on 4,948 adults aged ≥20 years from the Korean National Health and Nutrition Examination Survey V-3 (2012) were analyzed. After adjusting for the related variables (except age), the odds ratios (ORs) of vitamin D deficiency with the normal group as a reference were significantly higher in the decreased eGFR plus elevated uACR group [3.089 (95% CI, 1.722–5.544)], but not in the elevated uACR [1.247 (95% CI, 0.986–1.577)] and decreased eGFR group [1.303 (95% CI, 0.789–2.152)]. However, when further adjusting for age, the ORs of vitamin D deficiency with the normal group as a reference were significantly higher in the elevated uACR group [1.312 (95% CI, 1.035–1.662)], decreased eGFR group [1.761 (95% CI, 1.062–2.919)] and the decreased eGFR plus elevated uACR group [3.549 (95% CI, 1.975–6.365)]. In conclusion, vitamin D deficiency was positively associated with the elevated uACR and decreased eGFR. In addition, vitamin D level decreased greatly when decreased eGFR and elevated uACR appeared simultaneously.