Objective: High altitude polycythemia (HAPC) is a health condition associated with hypoxemia and erythrocytosis. Patients with chronic hypoxemia often exhibit arterial stiffness. In the advanced stages of HAPC, patients can present changes in the pulmonary circulation, but limited information exists regarding arterial stiffness. Our study aims to investigate the relationship between HAPC and arterial stiffness, and explore the underlying mechanisms. Design and method: At an altitude of 3500m, we conducted a study examining arterial stiffness and vascular endothelial function in two groups of hypertensive highlanders with and without HAPC, each consisting of 30 participants. Plasma samples were measured using Ultra Performance Liquid Chromatography Tandem Mass Spectroscopy. Results: Hypertensive highlanders with HAPC exhibited notable vascular dysfunction, as indicated by significantly impaired flow-mediated dilation (FMD) (3.97±1.21% vs. 6.82±1.46%, P < 0.001), and higher brachial-ankle pulse wave velocity (BaPWV) (1556±239 cm/s vs. 1890±459 cm/s, P < 0.001). Metabolomics analysis revealed alterations in arginine/proline metabolism and the arginine biosynthesis pathway, involving L-arginine, L-ornithine, creatine and 4-guanidinobutanoic acid. The area under the curve (AUC) values for 4 metabolites and L-arginine/L-ornithine ratio were 0.753, 0.782, 0.720, 0.717 and 0.819, respectively. Pearson correlation analysis showed that L-arginine, L-ornithine, and L-arginine/L-ornithine ratio were associated with BaPWV (r=-0.4486, P=0.00032; r=0.3400, P=0.0078; r=0.3921, P=0.0019). L-arginine, L-ornithine, 4-guanidinobutanoic acid, creatine, and L-arginine/L-ornithine ratio were correlated with FMD. Multiple linear regression analysis revealed that L-arginine and L-arginine/L-ornithine ratio were independently correlated with BaPWV (beta= -0.370, t=-3.114, P=0.003; beta=-0.268, t=-2.211, P=0.032) and FMD (beta=0.434, t=3.114, P=0.003; beta= 0.457, t=3.445, P=0.001), but L-ornithine was not independently related to BaPWV and FMD. Conclusions: Our study indicates that HAPC may accelerate the progression of arterial stiffness in hypertensive patients. In fact, L-arginine takes an important role in the forming of NO in vascular endothelium. So The disorder of arginine metabolism may serve as the underlying metabolic mechanism.