Metabolic syndrome (MetS) is a complex condition that significantly increases the risk of several diseases, including heart disease and diabetes. Patients with MetS show both pro-inflammatory and pro-thrombotic states; however, the state that takes precedence in MetS progression is unclear. The molecular mechanisms underlying the prodromal features in MetS have still not been well-elucidated. In this cohort-based study, we analyzed the characteristics of pre-MetS by dividing 100 participants into three groups: normal, pre-MetS, and MetS. We performed a systematic transcriptome analysis using RNA-seq data obtained from the peripheralbloodofindividuals. Geneexpressionand pathway enrichment analyses revealed that immune-related dysregulation was prominent in the pre-MetS group. In contrast, the MetS group showed significant coagulationrelated dysregulation. These results suggest that the pro-inflammatory state may be a prodromal feature of pre-MetS, followed by a pro-thrombotic state during progression to MetS. Our findings may contribute to the prevention of MetS progression by encouraging the development of diagnostic and therapeutic strategies that target the identified pre-MetS-associated genes and pathways.