The oxidized 1‐palmitoyl‐2‐arachidonoyl‐sn‐glycero‐3‐phosphocholine (ox‐PAPC) products in human high‐density lipoproteins (HDLs) were investigated by low‐flow capillary electrophoresis‐mass spectrometry (low‐flow CE‐MS). To accelerate the optimization, native PAPC (n‐PAPC) standard was first analyzed by a commercial CE instrument with a photodiode array detector. The optimal separation buffer contained 60% (v/v) acetonitrile, 40% (v/v) methanol, 20 mM ammonium acetate, 0.5% (v/v) formic acid, and 0.1% (v/v) water. The selected separation voltage and capillary temperature were 20 kV and 23°C. The optimal CE separation buffer was then used for the low‐flow CE‐MS analysis. The selected MS conditions contained heated capillary temperature (250°C), capillary voltage (10 V), and injection time (1 s). No sheath gas was used for MS. The linear range for n‐PAPC was 2.5–100.0 µg/mL. The coefficient of determination (R2) was 0.9918. The concentration limit of detection was 1.52 µg/mL, and the concentration limit of quantitation was 4.60 µg/mL. The optimal low‐flow CE‐MS method showed good repeatability and sensitivity. The ox‐PAPC products in human HDLs were determined based on the in vitro ox‐PAPC products of n‐PAPC standard. Twenty‐one ox‐PAPC products have been analyzed in human HDLs. Uremic patients showed significantly higher levels of 15 ox‐PAPC products than healthy subjects.