Background: The cellular composition and molecular mechanisms of the pathological arteries in Moyamoya disease (MMD) remain poorly understood. To improve our understanding of pathogenesis in MMD, we aimed to comprehensively map the cellular composition and molecular alterations within the pathological arteries of patients with MMD. Methods: Superficial temporal artery samples were collected from patients with MMD (n=2) and healthy controls (n=3), yielding a total of 26 371 cells that were used for single‐cell RNA sequencing. Differentially expressed genes, pathway enrichment, and cell–cell communication analyses were performed to examine disease‐related changes. In vitro experiments were performed to validate the changes in endothelial cells (ECs) and smooth‐muscle cells (SMCs), as well as the interactions between immune cells and ECs and SMCs. Results: We identified 8 major cell types in the human superficial temporal artery. We observed an increased proportion of SMCs in the superficial temporal artery of MMD. Two distinct SMC clusters, SMC1 and SMC2, were identified and exhibited different gene expression. Immune profiling revealed significant upregulation of genes in natural killer T cells, suggesting increased immune activity in MMD. Cell–cell communication analysis highlighted the role of the macrophage migration inhibitory factor pathway in promoting interactions between immune cells, SMCs, and ECs. In vitro experiments confirmed that the colocalization of CD74 with CD44 or CXCR4 in ECs promotes EC proliferation and angiogenesis. Natural killer T cells can promote cytoskeletal enlargement in ECs and SMCs, enhancing their migratory and proliferative capacities, as well as promoting angiogenesis in ECs. Conclusions: This study provides a single‐cell transcriptomic map of the superficial temporal artery in MMD, revealing key immune and vascular cell populations. Immune cells, particularly natural killer T cells, play a critical role in promoting SMC and EC proliferation and migration, contributing to vascular occlusion. These findings make contributions to understanding the pathogenesis of MMD and suggest potential therapeutic targets.

Moyamoya disease (MMD) is a cerebrovascular disease which can result in severe strokes. However, its etiology is still unknown. We analyzed gene expression datasets from 36 MMD patients and 24 controls to identify differentially expressed genes. Using weighted gene co-expression network analysis and databases such as KEGG, we identified hypoxia-immune-related genes. These genes were further refined through machine learning algorithms. The diagnostic value was confirmed using an external dataset, and a diagnostic nomogram was constructed. Additionally, gene set enrichment analysis was conducted, and a competitive endogenous RNA (ceRNA) network was built to predict potential therapeutic targets. Our study identified AKT1, CLDN3, ISG20, and TGFB2 as the key hypoxia-immune genes associated with MMD. These genes were implicated in epithelial–mesenchymal transition, angiogenesis, and cell adhesion, suggesting a role in MMD pathogenesis. Further, our study constructed the ceRNA network and predicted potential drug targets for MMD. We obtained the top 10 drugs in the interaction of the four key genes that might serve as potential targets for the treatment of MMD. In conclusion, this study comprehensively analyzes the role of hypoxia-immune genes in MMD, which is conducive to the development of new diagnostic and therapeutic approaches and the exploration of the potential pathogenesis of MMD.