Our study explored the association between subtypes of increased fat mass (with or without associated metabolic alterations) and the presence of chronic kidney disease (CKD).In this cross-sectional survey in China, body mass index (BMI) was used to assess fat mass. Metabolically healthy was defined as no insulin resistance or any metabolic syndrome components except abdominal obesity. We also used two previous definitions of metabolically healthy. Multiple logistic regression models were used. Normal weight with metabolic health was designated the reference group. Three other subgroups included normal weight with metabolic unhealthiness, overweight/obesity with metabolic health and overweight/obesity with metabolic unhealthiness.Of the 2324 subjects, 11.77% overweight/obese subjects were metabolically healthy. Compared with normal-weight subjects who were metabolically healthy, overweight/obese subjects who were metabolically healthy did not have an increased risk of CKD (OR: 0.79, 95% CI: 0.29–2.14; P = 0.64), whereas overweight/obese subjects who were metabolically unhealthy had a significantly higher risk of CKD (OR: 2.47, 95% CI: 1.5–3.95; P < 0.001). Normal-weight subjects who were metabolically unhealthy also had a higher risk of CKD, but the P value was of borderline significance. On further adjusting for C-reactive protein (CRP) levels, ORs were much attenuated, but did not alter the associations observed. Using two other definitions of metabolically healthy resulted in similar results.Metabolically unhealthy overweight/obesity, but not metabolically healthy overweight/obesity, is associated with an increased risk of CKD. Inflammation might mediate at least part of the association between metabolic changes and CKD prevalence.