Atomic oxygen and ozone are essential reactive species in plasma oxidation processes. Pure oxygen discharge is preferable to produce atomic oxygen and ozone while a difficulty in measuring their local densities exists. The ozone density is typically measured by UV absorption, but its resolution is insufficient for measuring the local ozone density in filamentary discharges. The atomic oxygen density can be measured by two-photon absorption laser-induced fluorescence (TALIF) method. However, ozone interference from the in situ atomic oxygen production due to ozone fragmentation by the incident UV light disturbs the TALIF measurement of the discharge-originated atomic oxygen. Therefore, compensation for ozone interference is necessary in atomic oxygen measurements. In this study, we propose a method to separate ozone interference from the discharge-originated atomic oxygen signal by focusing on different TALIF signal dependence on the laser intensity between atomic oxygen density and ozone density. By changing the laser intensity in the TALIF measurement, we separate the signal of atomic oxygen density from that of ozone interference. Under a short-gapped pulsed barrier discharge at a 3.1 mJ discharge energy, the gas temperature and the local densities of the atomic oxygen and ozone in the observed volume are estimated to be approximately 380 K, 3.8–11.3 , and 3.4 , respectively. This estimated atomic oxygen density is consistent with the absolute atomic oxygen density calibrated by the Xe-TALIF measurement. This consistency indicates that our method is applicable for absolute density measurements of atomic oxygen using ozone as the calibration reference.