Background/Aims: Cross-classification analyses are rarely reported. We investigated the prognostic factors for chronic kidney disease (CKD) progression using a body mass index (BMI)-based cross-classification approach. Methods: Patients’ renal outcome (≥50% decline in the estimated glomerular filtration rate or end-stage renal disease) in each subcohort was examined. Results: The number of prognostic factors identified in the multivariate Cox analysis was smaller in the “BMI ≥25, female” and CKD stage 3 subcohorts than in other subcohorts. Prognostic factors identified in the “BMI ≥25, CKD stage 3” subcohort only comprised albuminuria and male sex, and those in the “BMI ≥25, female” subcohort only comprised albuminuria, hyperphosphatemia, and anemia. Albuminuria, kidney impairment, male sex, hyperphosphatemia, anemia, and increased pulse pressure × heart rate product (PP × HR; pulsatile stress) were stable renal prognostic factors in almost all subcohorts. On the other hand, the prognostic value of increased BMI, younger age, hypoalbuminemia, increased intact parathyroid hormone, and decreased estimated 24-h urinary potassium excretion (e24hUK) differed according to subcohort. BMI was positively associated with CKD progression in the “BMI ≥25, age ≥65 years” and “BMI ≥25, CKD stages 4–5” subcohorts, whereas it was negatively associated with CKD progression in the “BMI <25, diabetes mellitus” subcohort. PP × HR was independently associated with CKD progression in the “BMI <25, CKD stage 3” subcohort, which had relatively few identified renal prognostic factors. Decreased e24hUK was a renal prognostic factor for CKD progression in the “BMI <25, CKD stages 4–5” subcohort, while no significant factors were observed in the “BMI ≥25, CKD stages 4–5” subcohort. Conclusion: A BMI-based cross-classification approach, which provides more comprehensive findings than that in previous approaches, is expected to be an effective method for evaluating renal prognostic factors in patients with CKD who are affected by multiple risk factors.