Partitioning soil CO2 efflux into autotrophic (RA) and heterotrophic (RH) components is crucial for understanding their differential responses to climate change. We conducted a long-term experiment (2000–2005) to investigate effects of warming 2°C and yearly clipping on soil CO2 efflux and its components (i.e. RA and RH) in a tallgrass prairie ecosystem. Interannual variability of these fluxes was also examined. Deep collars (70 cm) were inserted into soil to measure RH. RA was quantified as the difference between soil CO2 efflux and RH. Warming treatment significantly stimulated soil CO2 efflux and its components (i.e. RA and RH) in most years. In contrast, yearly clipping significantly reduced soil CO2 efflux only in the last 2 years, although it decreased RH in every year of the study. Temperature sensitivity (i.e. apparent Q10 values) of soil CO2 efflux was slightly lower under warming (P>0.05) and reduced considerably by clipping (P<0.05) compared with that in the control. On average over the 4 years, RH accounted for approximately 65% of soil CO2 efflux with a range from 58% to 73% in the four treatments. Over seasons, the contribution of RH to soil CO2 efflux reached a maximum in winter (∼90%) and a minimum in summer (∼35%). Annual soil CO2 efflux did not vary substantially among years as precipitation did. The interannual variability of soil CO2 efflux may be mainly caused by precipitation distribution and summer severe drought. Our results suggest that the effects of warming and yearly clipping on soil CO2 efflux and its components did not result in significant changes in RH or RA contribution, and rainfall timing may be more important in determining interannual variability of soil CO2 efflux than the amount of annual precipitation.