Abstract: Metabolic diseases, represented by diabetes mellitus, metabolic dysfunction-associated fatty liver disease, obesity and atherosclerotic cardiovascular disease, often co-occur clinically and share a common pathological basis. The concept of “pan-lipotoxicity” overcomes the limitations of traditional lipotoxicity, which focuses on localised lipid deposition, by emphasising that lipid metabolism disorders constitute a ubiquitous toxic state characterised by diverse pathogenic components and a broad pathological scope. Based on the Traditional Chinese Medicine (TCM) theory of Gaozhi-Sanjiao, and guided by the concept of “pan-lipotoxicity”, we treat metabolic diseases through the common origin-common mechanism-common treatment Three-Commonality theory. The rationale can be summarized as follows: the non-transformation of Gaozhi and stagnation of Sanjiao serve as the origin of same pathogenesis; the pervasive diffusion and transmission of turbid toxicity along the Sanjiao pathway constitute the pivotal mechanism; and the principles of unblocking Sanjiao and dispersing turbid toxicity represent the corresponding therapeutic approach. This article systematically elucidates the comorbidity mechanisms and progression patterns of metabolic diseases from the perspective of “pan-lipotoxicity”, structuring the discussion around the same origin-same mechanism-same treatment framework. It establishes a trinity differentiation and treatment system based on the Gaozhi-Sanjiao theory, thereby providing a systematic TCM theoretical framework for the comprehensive prevention and treatment of metabolic diseases.