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Background Diabetic nephropathy (DN) accounts for approximately half of all cases of chronic kidney disease (CKD) and end-stage kidney disease worldwide. The Renal Pathology Society (RPS) classification has been used to predict the renal prognosis in DN. In 2018, the Japanese Renal Pathology Society (JRPS) proposed a comprehensive classification system that included pathological changes in the kidney. The clinical significance of the JRPS classification system was comparatively evaluated in the present study. Methods A total of 93 cases diagnosed with DN from 2009 to 2019 were enrolled. JRPS scores (J-scores) were calculated by scoring the pathological factors in the JRPS classification system and comparing them with clinical parameters. Results Most pathological factors constituting the J-score were significantly correlated with clinical factors. Laminated nodules were inversely correlated with estimated glomerular filtration rate. After adjusting for age, sex, body mass index, hemoglobin A1c, diabetes duration, and hypertension, CKD stage was significantly correlated with JRPS grade, nodular lesions, and exudative lesions in the multivariate logistic regression analysis. However, receiver operating characteristic curve analysis revealed that the J-score (area under the curve [AUC] = 0.639) had lower clinical significance than the traditional RPS classification system (AUC = 0.675). Conclusion The JRPS classification can more comprehensively reflect renal changes than the RPS classification and is correlated with renal survival. When creating a new pathological classification, arteriolar hyalinosis should not be included, whereas laminated nodules should be included.