Abstract <p>Previous studies have established a correlation between the microbiome-derived metabolite trimethylamine <i>N</i>-oxide (TMAO) and decreased renal function, but with great heterogeneity. Moreover, population-based evidence remains scarce, particularly in Chinese populations. We designed a meta-analysis and a population-based cross-sectional study in China to examine the associations between TMAO and chronic kidney disease (CKD). In meta-analysis, among 2125 pooled subjects with 1240 controls and 885 CKD patients, a significant association was observed between TMAO and CKD, with a standardized mean difference of − 0.93 (95% confidence interval: − 1.11, − 0.75). Meta-regression analysis identified gender, age, and body mass index (BMI) as significant heterogeneity factors. In our population-based study of 5584 subjects with an estimated glomerular filtration rate (eGFR) ≥ 60 mL/min/1.73 m² from Sijing community, 100 developed CKD in 2&#xa0;years. We matched 195 controls by age and gender from the 5484 non-CKD subjects. Male subjects and alcohol consumers exhibited a lower risk of CKD with adjusted odds ratio (OR) of 0.471 (<i>P</i> &lt; 0.05) and 0.320 (<i>P</i> &lt; 0.05), respectively. When comparing subjects in the lowest tertile of TMAO, adjusted OR reached to 1.243 (<i>P</i> &gt; 0.05) for those in the middle and 2.123 (<i>P</i> &lt; 0.05) in the highest tertile (<i>P</i> for trend &lt; 0.05). TMAO demonstrated a moderate capacity to distinguish CKD from non-CKD subjects (AUC = 0.614, <i>P</i> &lt; 0.01). Our findings indicate TMAO is significantly associated with the risk of CKD, and suggest age, gender, and BMI may confound the relationship between TMAO and CKD.</p> Key points <p><i>• Subjects with elevated TMAO levels have an increased risk of CKD.</i></p> <p><i>• TMAO demonstrates a moderate capacity to distinguish CKD from non-CKD cases.</i></p> <p><i>• Age, gender and BMI may confound the relationship between TMAO and CKD.</i></p>