We investigated the potential effects of elevated ozone (O3) along with climate variability, increasing CO2, and land use change on net primary productivity (NPP) and carbon storage in China's terrestrial ecosystems for the period 1961–2000 with a process-based Dynamic Land Ecosystem Model (DLEM) forced by the gridded data of historical tropospheric O3 and other environmental factors. The simulated results showed that elevated O3 could result in a mean 4.5% reduction in NPP and 0.9% reduction in total carbon storage nationwide from 1961 to 2000. The reduction of carbon storage varied from 0.1 Tg C to 312 Tg C (a decreased rate ranging from 0.2% to 6.9%) among plant functional types. The effects of tropospheric O3 on NPP were strongest in east-central China. Significant reductions in NPP occurred in northeastern and central China where a large proportion of cropland is distributed. The O3 effects on carbon fluxes and storage are dependent upon other environmental factors. Therefore direct and indirect effects of O3, as well as interactive effects with other environmental factors, should be taken into account in order to accurately assess the regional carbon budget in China. The results showed that the adverse influences of increasing O3 concentration across China on NPP could be an important disturbance factor on carbon storage in the near future, and the improvement of air quality in China could enhance the capability of China's terrestrial ecosystems to sequester more atmospheric CO2. Our estimation of O3 impacts on NPP and carbon storage in China, however, must be used with caution because of the limitation of historical tropospheric O3 data and other uncertainties associated with model parameters and field experiments.