Metabolic-associated fatty liver disease (MAFLD), a globally prevalent chronic liver disorder, is characterized by a dynamically progressive disease spectrum spanning simple hepatic steatosis, steatohepatitis, and hepatic fibrosis/cirrhosis. Although Western medicine has clarified its "multiple hits" pathogenesis, specific therapeutic strategies for MAFLD are lacking and primarily rely on lifestyle interventions and limited medications and pharmacotherapies. Although the traditional syndrome differentiation of Chinese medicine focuses on pathological factors, such as phlegm-dampness and blood stasis, it has certain limitations in systematically capturing the complex dynamic evolutionary process of this disease from functional disorder to organic damage, thereby limiting its clinical efficacy in prevention and treatment. This study proposes a core pathogenesis evolution law of MAFLD characterized by stagnation to impairment. It clarifies that the disease undergoes a three-stage dynamic progression following the stagnation pathway (qi movement stagnation)→ heat (turbid toxin transforming into heat)→ impairment (hepatic injury with fibrosis and mass formation). Our team have established a three-stage and three-dimension stereoscopic pathogenesis model, in which the vertical dimension delineates the temporal progression of the disease through the stagnation, heat, and impairment stages, and the horizontal dimension deciphers the core targets of each stage from three aspects: zang-fu viscera function, pathological factors, and collateral status, forming a spatiotemporally integrated pathogenesis analysis system. On this basis, we established a stage-specific diagnosis and treatment system featuring a three-step liver modulation strategy of dispersing stagnated liver qi, removing liver-fire, and nourishing the liver. We identified the representative herbal formulas corresponding to each stage. This three-stage, three-dimension diagnosis and treatment system achieved organic integration of pathogenesis understanding, syndrome differentiation, therapeutic principles and methods, and herbal formula application. It provides a novel theoretical framework and clinical approach for integrating Chinese and Western medicine to prevent and treat MAFLD, aiming to halt disease progression, improve patient prognosis, and address practical clinical challenges such as ambiguous disease staging, imprecise syndrome differentiation, and insufficient therapeutic targeting.