Ambient ozone is a common pollutant in the atmosphere that has an extremely high oxidative ability, can dramatically change the structure and functionality of biomolecules, and is harmful to public health. However, the knowledge about the influence of low-level ozone is still very limited at a molecular level. In the present study, the monolayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC, 16:0-18:1 PC) as well as its binary mixed monolayer with 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC, 16:0 PC), which are widely found in many biological systems, have been systematically investigated in a low-level ozone environment (20 ± 10 ppb), by π-A isotherm, sum frequency generation (SFG) vibrational spectroscopy, and atomic force microscopy (AFM). Our results demonstrate that the POPC monolayer is unstable and the C=C moieties in the oleyl chain are selectively oxidized by the low-level ozone. The oxidized lipids from POPC initially remain and reorientate the hydrophilic portion to the water surface and gradually dissolve into the aqueous solution. One should take great caution when using unsaturated lipid molecules to avoid their possible oxidation in the ambient environment. The present study expands and deepens our insights into the oxidation mechanism of unsaturated lipids at a molecular level.