This study aimed to examine the relationship between nutrition intake and estimated glomerular filtration rate (eGFR) indicating kidney function in Korean individuals without diabetes or cardiovascular disease. Study participants from the Korea National Health and Nutrition Examination Survey 2013–2014 (n = 4,378, 30–65 years) were classified by their eGFR levels (mL/min/1.732 m²): ≥ 120 (n = 299), 119–105 (n = 789), 104–90 (n = 1,578), 89–60 (n = 1,685), < 60 (n = 27). After adjusted for confounding factors (age, sex, cigarette smoking, alcohol drinking, total caloric intake [TCI], income status, education level, body mass index, and physical activity), blood pressure, low-density lipoprotein (LDL) cholesterol, aspartate aminotransferase, alanine aminotransferase, blood urea nitrogen, creatinine, fasting glucose, and glycated hemoglobin were higher, and high density lipoprotein cholesterol levels were lower in participants with lower eGFR levels than those with higher eGFR levels. n-3 fatty acid (FA) and n-6 FA (% of TCI/day) intake were also significantly higher in participants with higher eGFR levels than in those with lower eGFR levels. Based on the above results, participants were subdivided into 3 groups according to n-6 FA intake levels (Q1: ≥ 2.93%, n = 1,462; Q2: 2.92%–1.88%, n = 1,463; Q3: < 1.88%, n = 1,453). People consuming higher n-6 FAs, particularly the Q1 group showed higher eGFR levels and lower levels of LDL cholesterol and creatinine. In conclusion, higher intake of n-6 FAs within the range of dietary reference may be beneficial to maintain healthy kidney function.