Ozone (O3) is one of the most critical pollutants affecting air quality in China in recent years. In this study, different impacts of the El Niño–Southern Oscillation (ENSO) warm/cold phases on summertime tropospheric O3 over China are examined based on model simulations, ground measurements, and reanalysis data. Summertime surface O3 concentrations in China show a positive correlation with ENSO index during years 1990–2019, with the largest increases by 20% over southern China in El Niño (warm phase) relative to La Niña (cold phase) years. The ENSO modulation extends to the middle and even upper troposphere. Our analysis indicates that O3 flux convergence associated with weakened southerlies is the primary reason for the increase in tropospheric O3 over southern China. In addition, the O3 increase during El Niño years is mainly from domestic emissions in China. This study highlights the potential significance of ENSO in modulating tropospheric O3 concentrations in China, with great implications for O3 pollution mitigation.