We aimed to determine the magnitude, direction, and influencing factors of the concordance between arterial oxygen saturation (SaO2) and peripheral capillary oxygen saturation (SpO2) in patients with obesity undergoing bariatric surgery, supporting the measurement of SaO2 and SpO2 in key populations. Patients with obesity undergoing bariatric surgery from 2017 to 2020 were included. Preoperative SpO2 and SaO2 were collected. Linear correlation and multiple linear regression analyses were performed to characterize the relationships between body mass index (BMI), age, and sex with pulse oximetry and arterial blood gas (ABG) parameters. Bland-Altman analysis was applied to determine the concordance between SpO2 and SaO2 and the limits of this concordance. A total of 134 patients with obesity undergoing bariatric surgery were enrolled. SaO2 was negatively associated with BMI (p < 0.0001) and age (p = 0.006), and SpO2 was negatively associated with BMI (p = 0.021) but not with age. SpO2 overestimated SaO2 in 91% of patients with a bias of 2.05%. This bias increased by 203% in hypoxemic patients compared with nonhypoxemic patients (p < 0.0001). The bias was 1.3-fold higher (p = 0.023) in patients with a high obesity surgery mortality risk score (OS-MRS) than in those with low or intermediate scores. Compared with SpO2, preoperative SaO2 can more accurately reflect the real oxygen saturation in patients with obesity undergoing bariatric surgery, especially for those with BMI ≥ 40kg/m2, age ≥ 40years, and high OS-MRS. ABG analysis can provide a more reliable basis for accurate and timely monitoring, ensuring the perioperative safety of susceptible patients.