The polysomnography (PSG) index of the apnea hypopnea index (AHI) is considered the 'gold standard' for stratifying the severity of obstructive sleep apnea (OSA). However, AHI cannot reflect the true characteristic of chronic intermittent hypoxia (CIH), which may trigger systemic inflammation in some OSA patients. High-sensitivity C-reactive protein (hsCRP) is considered a biomarker of systemic inflammation in OSA patients. The aim of the present study was to evaluate the relationship between PSG variables and hsCRP in men with severe OSA. Men with severe OSA (AHI ≥ 30 events/h) diagnosed by PSG were enrolled. AHI and body mass index were matched between a high hsCRP group (hsCRP ≥ 3.0 mg/L) and a low hsCRP group. A blood sample was taken for serum hsCRP analysis. Multiple regression analysis was performed to assess independent predictors of high hsCRP. One hundred and fifty-two subjects were enrolled in the study (76 in each group). Mean serum hsCRP was 3.76 ± 2.13 mg/L. The mean percentage of total sleep time spent with SaO2 <90% (TST) in the high hsCRP group was significantly higher than in the low hsCRP group (20.99 ± 18.52 vs. 5.84 ± 7.30, p < 0.001). Multivariate analysis showed that TST was the strongest predictor, contributing to 27.7% of hsCRP variability (β = 0.496, p < 0.01). TST may be superior to AHI for evaluating CIH among OSA patients. The severity of OSA should be stratified by a combination of AHI and other hypoxia variables.