Although knowledge of the impact of N enrichment on soil C fluxes is scant, such information is highly critical for estimating the global C budget under elevated N deposition. To quantify the effects of short-term N addition on soil C sequestration in an alpine scrub ecosystem, we conducted a field experiment for Sibiraea angustata scrub on the eastern margin of the Qinghai-Tibetan Plateau in China. We quantified the soil C pool (0–30cm) and C fluxes in litterfall, fine root (<2mm diameter) production (FRP), and soil CO2 emission (heterotrophic respiration, Rh) over four years with four levels of N addition (N0; control, N20; 20, N50; 50, and N100, 100kgNha−1year−1). The results showed that at control plots the total C-input (433±33gCm−2year−1) via FRP (360±34gCm−2year−1) and litterfall (73±1gCm−2year−1) was close to the C-output via Rh (466±5gCm−2year−1), which demonstrates that the S. angustata scrub soil C is at equilibrium status. However, adding N, particularly the N100 treatment, significantly affected the soil C balance; the soil became a C sink (163±46gCm−2year−1) by increasing FRP (+63%) rather than by increasing litterfall (P>0.05) or reducing Rh (P>0.05). As a result, the soil C pool (0–30cm) increased significantly. In conclusion, these results suggest that fine roots play a dominant role in the C balance of an alpine scrub ecosystem due to large C-inputs to the soil. Moreover, short-term high N enrichment causes sequestration of additional atmospheric CO2, largely because of the stimulation of fine root growth rather than increased inputs of aboveground plant litterfall or reductions in soil CO2 emission.