This paper constructs a microscopic three-collateral syndrome differentiation model for the kidney, comprising qi-, blood-, and fluid-collateral (three-collaterals), which is grounded in the collateral disease theory and integrated with the kidney′ s microscopic structural and functional characteristics. Adopting the principle of "observing the collateral through microscopy and inferring the zang organs from manifestations," this study interprets morphological alterations in renal tissue observed under light and electron microscopy as "microscopic manifestations." It systematically elucidates the physiological functions and pathological signs of the three collaterals and establishes their correspondence with characteristic renal pathological changes. Drawing upon the "three-dimensional stereoscopic collateral network system" framework, this study reveals the dynamic progression patterns of renal collateral pathology across three dimensions: spatial, temporal, and functional. We propose an integrated diagnostic and therapeutic strategy of "differentiated treatment of the three collaterals with holistic network regulation," exemplified by the wind-damp disturbing the kidney syndrome in primary glomerulopathy. Regulating the qi-collateral primarily involves dispelling wind and eliminating dampness, benefiting qi, and stabilizing the collaterals. A modified Fangji Huangqi Decoction is used as the principal formula to protect the glomerular filtration barrier, restore the kidney′s function of storage and containment, and intercept pathogenic factor transmission and progression. Regulating the blood-collateral emphasizes removal of stasis at different pathological levels, dispersal of nodules, and elimination of static masses: mild cases are treated with Taohong Siwu Decoction to invigorate blood and harmonize the collaterals. Severe cases are treated with modified Jixuecao Formula to resolve stasis and dissolve micro-masses. Acute presentations are treated with integrated Chinese and Western medicine to intercept and reverse acute damage to the blood-collateral. Regulating the fluid-collateral prioritizes resolving turbidity, eliminating dampness, and supporting qi transformation, with Wuling Powder and Zhenwu Decoction as the principal formulas; in clinical practice, they promote blood circulation and induce diuresis herbs to facilitate collateral circulation, combined with Chaihu (Bupleuri Radix)-based formulas to regulate the sanjiao, and supplemented with Dahuang (Rhei Radix et Rhizoma) and Huzhang (Polygoni Cuspidati Rhizoma et Radix) to promote bowel movement and expel turbid toxins. Although each approach has a distinct emphasis, they act synergistically to form an integrated therapeutic framework, offering a novel theoretical pathway for microscopic syndrome differentiation and precision intervention in chronic kidney disease within the traditional Chinese medicine paradigm.