BACKGROUND: Systemic sclerosis (SSc) is an autoimmune disease characterized by vascular injury and progressive fibrosis. Although microvascular injury is an inciting event and pericytes are recognized as a major source of myofibroblasts, the precise phenotypic heterogeneity of pericytes in the SSc microenvironment and the genetic mechanisms driving their pathological transition remain elusive. METHODS: This study systematically explored the cellular and genetic basis of pericyte dysfunction by integrating single-cell RNA sequencing (scRNA-seq) data from SSc patients with genome-wide association study (GWAS) data using bidirectional Mendelian randomization (MR) analysis. Pseudotime trajectory analysis was used to reconstruct developmental lineages, while cell-cell communication and metabolic pathway analyses were conducted to uncover underlying mechanisms. Multiomics validation was performed using external bulk RNA-seq datasets. RESULTS: Single-cell analysis revealed significant heterogeneity in pericyte subpopulations, specifically identifying a marked expansion of progenitor-like pericytes, which were positioned at the root of the differentiation trajectory toward fibrotic phenotypes. Bidirectional MR analysis identified RAC1 as a significant causal risk factor for SSc (OR = 2.0756, p  = 0.0046). Mechanistically, RAC1-positive pericytes exhibited enhanced proinflammatory crosstalk with macrophages via the MIF-(CD74 + CD44) signaling axis. Furthermore, these activated pericytes displayed distinct metabolic reprogramming, characterized by the upregulation of riboflavin and thiamine metabolism to support their bioenergetic demands. Transcriptomic validation further confirmed the aberrant overexpression of RAC1 in SSc tissues. CONCLUSION: This study establishes a mechanistic link between RAC1-mediated activation of progenitor-like pericytes and SSc pathogenesis. RAC1 acts as a causal driver promoting pathological pericyte transition and orchestrates a proinflammatory microenvironment through metabolic reprogramming and immune recruitment, offering a novel therapeutic target for SSc.