Background: Weight loss-centered lifestyle remains a first-line intervention for non-alcoholic fatty liver disease (NAFLD). However, whether weight loss benefits adverse kidney outcomes is uncertain. Therefore, we aimed to investigate baseline and changes in obesity measures on chronic kidney disease (CKD) risks after NAFLD occurrence. Methods: We enrolled 10311 adult men with newly diagnosed NAFLD and without CKD in the Kailuan cohort in 2006–2013. The Fine and Gray competing risk regression model was used to compare the advanced CKD risk in NAFLD with different baseline or trajectories in obesity measures after 1–4 years of NAFLD diagnosis. Findings: During a median follow-up of ten years, baseline body mass index (BMI), waist circumference (WC), and waist-hip ratio (WHR) were not observed associated with CKD development for incident NAFLD subjects. Maintaining WC or WHR, or transition from obese to nonobese determined by the BMI decreased a 31% [95% confidence interval (CI): 0·51–0·93], 34% (95% CI: 0·45–0·95), and 38% (95% CI: 0·40–0·96) of the CKD hazard compared to the corresponding constantly normal subgroup, respectively. In addition, NAFLD individuals with ≥10% weight loss (HR=0 · 58, 95%CI: 0·34–0·97) and 7·0%–9·9% weight loss (HR=0·53, 95% CI: 0·28–0·99) had a lower risk for CKD than those with weight change ± 4·9%. Interpretation: Short-term weight loss or keeping WC or WHR was associated with a lower risk of CKD for patients with incident NAFLD. Our findings, if verified by more research with long-term prospective cohort study, suggest the importance of monitoring WC, WHR, and weight for newly diagnosed NAFLD patients' management. Funding: This work was supported by CAMS Innovation Fund for Medical Sciences (CIFMS) (2016-I2M-3-001 and 2019-I2M-2-007). Declaration of Interest: We declare that we have no conflicts of interest. Ethical Approval: This study was approved by the Ethics Committees of the Kailuan General Hospital and the Institute of Basic Medical Sciences Chinese Academy of Medical Sciences.