This study examined the effect of Pilates training under hypoxia, a novel treatment method, for obesity. Thirty-two Korean women with obesity (age: 34–60 (47.5 ± 7.5) years) were randomly assigned to control (CON; n = 10), normoxic Pilates training (NPTG; n = 10), and hypoxic Pilates training groups (HPTG; n = 12). The NPTG and HPTG performed 50 min of Pilates training using a tubing band for 12 weeks (3 days/week) in their respective environmental conditions (NPTG: normoxic condition, inspired oxygen fraction (FiO2) = 20.9%; HPTG: moderate hypoxic condition, FiO2 = 14.5%). The CON maintained their daily lifestyle without intervention. All subjects underwent body composition, blood pressure, arterial stiffness, vascular endothelial function, cardiometabolic biomarker, hemorheological function, and aerobic performance measurements before and after the intervention. The HPTG showed a significant improvement in diastolic blood pressure, total cholesterol and triglyceride concentrations, flow-mediated dilation, and erythrocyte deformability and aggregation (all p < 0.05) compared with the CON and NPTG. However, compared with the CON and NPTG, the HPTG did not show improvement in other parameters. Hypoxic Pilates intervention is a novel and successful method for promoting endothelial and hemorheological functions in women with obesity.