We investigated how ozone pollution and climate change/variability have interactively affected net primary productivity (NPP) and net carbon exchange (NCE) across China's forest ecosystem in the past half century. Using the dynamic land ecosystem model (DLEM) in conjunction with 10-km-resolution gridded historical data sets (tropospheric O3 concentrations, climate variability/change, and other environmental factors such as land-cover/land-use change (LCLUC), increasing CO2 and nitrogen deposition), we conducted nine simulation experiments to: (1) investigate the temporo-spatial patterns of NPP and NCE in China's forest ecosystems from 1961–2005; and (2) quantify the effects of tropospheric O3 pollution alone or in combination with climate variability and other environmental stresses on forests' NPP and NCE. China's forests acted as a carbon sink during 1961–2005 as a result of the combined effects of O3, climate, CO2, nitrogen deposition and LCLUC. However, simulated results indicated that elevated O3 caused a 7.7% decrease in national carbon storage, with O3-induced reductions in NCE (Pg C year−1) ranging from 0.4–43.1% among different forest types. Sensitivity experiments showed that climate change was the dominant factor in controlling changes in temporo-spatial patterns of annual NPP. The combined negative effects of O3 pollution and climate change on NPP and NCE could be largely offset by the positive fertilization effects of nitrogen deposition and CO2. In the future, tropospheric O3 should be taken into account in order to fully understand the variations of carbon sequestration capacity of forests and assess the vulnerability of forest ecosystems to climate change and air pollution. Reducing air pollution in China is likely to increase the resilience of forests to climate change. This paper offers the first estimate of how prevention of air pollution can help to increase forest productivity and carbon sequestration in China's forested ecosystems.