Drought and extreme precipitation are projected to occur more frequently as a consequence of climate change, with uncertain implications for soil CO2 emission. Although studies have revealed the response patterns of soil CO2 emission to precipitation pulse, the effects of forest plant roots on this relationship after drought are still poorly understood. Here, a field experiment was performed to examine the differences in soil CO2 emission and microbial community between rootless and rooted soils, pretreated with three drought intensities (control, moderate, and severe), and rewetted with different water additions (0, 5, 10, and 20 mm) in a temperate forest. Compared with control soils, whether the water was added or not, severe drought suppressed soil CO2 emission for both root-excluded and -included soils. Regardless of drought intensities, significantly positive effects (19.4–44.9%) of precipitation pulse on soil CO2 emission were only detected in the root-included soils. Both the contribution of root-derived CO2 to the stimulated soil CO2 emission and biomass of soil arbuscular mycorrhizal fungi (AMF) substantially increased with elevated precipitation levels. The enhanced soil CO2 emission following precipitation pulse is primarily due to the increase in root-derived CO2 in the rooted soils, likely resulting from the enhanced biomass of soil AMF. This study provides empirical evidence on the primacy of AMF in root-derived CO2 and thus the response of soil CO2 emission to precipitation pulse in forest ecosystems.