Background Urine examination can reflect concealed kidney diseases in children. However, few surveys described the difference in urine routine indicators between children belonging to different ethnic groups. This study aimed to compare urine components between Han and Tibetan preschool children in western China and explore influencing factors for early kidney disease prevention.MethodsThe urine routine data were obtained by cluster sampling of children (N = 1645: NHan = 1019, NTibetan = 626, age range: 0–6 years) in 10 child care institutions of Lanzhou City and Gannan Tibetan Autonomous Prefecture through the medical examination center affiliated to a top three hospital in Gansu Province in western China. The correlation of the urine routine indicators with the factors, including living environment, diet, family income, and kidney disease in parents, were explored through multiple logistic regression analysis.ResultsThe lower age group (1–3 years old) was a protective factor for urinary vitamin C in Han children [odds ratio (OR) Han = 0.13, 95% confidence interval (CI) = 0.05–0.32], while it was a risk factor among Tibetan children (OR Tibetan = 3.01, 95% CI = 1.28–7.10), compared with the higher age group (4–6 years old). Among Han children, male sex was the risk factor for urinary ketone body (OR Han = 2.28, 95% CI = 1.20–4.33). Among Tibetan children, living in newly decorated houses was a risk factor for urinary ketone body and urinary occult blood (OR ketone body = 2.35, 95% CI = 1.12–4.93; ORoccult blood = 18.20, 95% CI = 4.30–76.92). Male sex is the protective factor for urinary leukocyte detection in both Han and Tibetan children (OR Han = 0.10, 95% CI = 0.04–0.20; ORTibetan = 0.25, 95% CI = 0.10–0.63). The intake of lead-containing foods is a risk factor for urinary leukocyte detection in Tibetan children (ORTibetan = 4.34, 95% CI=1.19–15.91). Parental kidney disease history is a risk factor for urinary occult blood in Han children (ORHan = 2.56, 95% CI=1.21–5.41).ConclusionThe differences in physiology, diet, and living environment in children belonging to different ethnic groups were influencing factors for different urine abnormalities.