Rapid climate warming, permafrost degradation and widespread vegetation improvement on the Qinghai-Tibet Plateau (QTP) have caused carbon input via photosynthesis and carbon output through soil respiration to significantly increase in recent decades; thus, its role as a carbon sink/source is unclear and highly disputed, especially at different soil depths. In this study, we took the Qinghai Plateau (northeastern QTP), with an area of 7.2 × 105 km2 (permafrost accounts for 52% of the land) and an elevation ranging from 1669 m to 6548 m, as the study region and estimated its spatial pattern of soil organic carbon (SOC) stock changes at different soil depths from the 1980s to 2010s. The paired site observations of the SOC stocks in the 1980s from the second national soil survey and in the 2010s from a field survey and the literature were compiled and then combined with 77 related environmental factors to drive multiple machine learning models (random forest, gradient-boosting machine, and Cubist), from which the spatial patterns of SOC stock changes at different soil depths (0–30, 30–50, and 50–100 cm) were revealed. The results indicated that the SOC stock increased in the soil at 0–100 cm over the past three decades, with a mean net accumulation rate of 7.36 g C m−2 yr−1 or a total of 0.153 Pg C. Compared with seasonally frozen soil, more significant increases in the SOC stock were observed in permafrost at the 0–100 cm depth (9.71 vs. 4.81 g C m−2 yr−1). However, the SOC stock changes in different soil layers showed significant differences. Specifically, the SOC stock substantially increased in the topsoil layer (0–30 cm), with a carbon increase of 7.82 g C m−2 yr−1; the SOC stock in the middle layer (30–50 cm) had a slight increase, with a carbon increase of 1.69 g C m−2 yr−1; and the SOC stock decreased in the bottom layer (50–100 cm), with a net carbon loss rate of 2.15 g C m−2 yr−1. We found that vegetation change was the key driver of SOC stock change in the topsoil layer. With the increase in soil depth, the importance of climate change on SOC stock change increased. We concluded that climate-driven carbon losses in the deep soil layer were offset by an increase in vegetation-driven carbon inputs at the top and middle soil layers, triggering plant-dominated negative soil carbon feedback to climate warming. With the temperature continuing to increase, however, we must pay more attention to the risk of carbon release in the middle and bottom soil layers.