Currently, there are no established objective and sensitive diagnostic methods in traditional Chinese medicine (TCM) to differentiate dampness constitution (DC), which is often caused by prolonged exposure to an improper diet or a humid environment. These factors trigger chronic, immune and metabolic diseases, posing a significant threat to human health. In this study, we obtained high-quality serum exosome proteins and conducted proteome profiling across two cohorts. Cohort 1 included 20 healthy subjects, with a balanced constitution (BC, n = 10) and DC (n = 10), to characterize the protein basis of DC. Cohort 2 comprised a clinical randomized controlled trial investigating the treatment of dampness-related hyperlipidemia (DC-hyperlipidemia) using Fuling Zexie decoction (FLZXD). By comparing this cohort with the BC group, the study assessed the efficacy of FLZXD in treating DC-hyperlipidemia. The active components of FLZXD, identified through extensive patent experiments and pharmacological evidence, including Fuling, Zexie, and Baizhu. We successfully identified and validated four targets related to the diagnosis and treatment of DC-hyperlipidemia. This study confirms that DC is distinguishable through serum-derived exosome proteomics and can be reversed through herbal treatment. This diversification strategy has validated our characterization of the DC, offering a paradigm for research in TCM constitution with significant clinical implications.