Obesity and chronic kidney disease (CKD) are major global health problems. There are very little data concerning the prevalence and its associated factors of obesity in non-dialyzed patients who have different stages of CKD. Therefore, in this study, we examined the prevalence of obesity and its associated factors according to the stages of CKD. We used nationwide representative data from the Korean National Health and Nutrition Examination Survey, which was conducted over a 7-year period from 2008 to 2014 by the Korea Centers for Disease Control and Prevention. The results indicated that: (1) general obesity and abdominal obesity were more prevalent in patients with CKD compared to those without CKD; (2) the prevalence of general obesity and abdominal obesity was highest in stage 2 CKD; (3) stages 3a and 3b were the factors associated with general obesity, and stage 3a was significantly associated with abdominal obesity; (4) the association between general obesity/abdominal obesity and CKD disappeared in people with advanced stage 4/5 CKD; and (5) the presence of comorbidities contributed to the development of both general obesity and abdominal obesity. The findings of this study might support the idea that weight loss is a good potential intervention for the prevention of disease progression in moderate CKD (stage 3), but not severe CKD (stage 4/5).