Differentiating between diabetic nephropathy (DN) and non-diabetic renal disease (NDRD) without a kidney biopsy remains a major challenge, often leading to missed opportunities for targeted treatments that could greatly improve NDRD outcomes. To reform the traditional biopsy-all diagnostic paradigm and avoid unnecessary biopsy, we developed a transformer-based deep learning (DL) system for detecting DN and NDRD upon non-invasive multi-modal data of fundus images and clinical characteristics. Our Trans-MUF achieved an AUC of 0.980 (95% CI: 0.979 to 0.980) over the internal retrospective set and also had superior generalizability over a prospective dataset (AUC: 0.989, 95% CI: 0.987 to 0.990) and a multicenter, cross-machine and multi-operator dataset (AUC: 0.932, 95% CI: 0.931 to 0.939). Moreover, the nephrologists' diagnosis accuracy can be improved by 21%, through visualization assistance of the DL system. This paper lays a foundation for automatically differentiating DN and NDRD without biopsy. (Registry name: Correlation Study Between Clinical Phenotype and Pathology of Type 2 Diabetic Nephropathy. ID: NCT03865914. Date: 2017-11-30).