Seasonally frozen ground (SFG) significantly contributes to global carbon sinks. Global warming and anthropogenic-induced disturbances threaten the carbon storage capacity of SFG. Challenges in evaluating the SFG carbon storage potential include the lack of understanding of the control mechanisms of soil organic carbon (SOC) variations and timely spatial estimates of SOC. In this study, we investigated SOC stocks in SFG in the Tibet Autonomous Region, China, in 2020 and 2021. We employed partial least squares structural equation modeling (PLS-SEM) to explore the effect of complex processes (interacting roles of climate, plant physiology and phenology, freeze–thaw cycle, soil environment, and C inputs) on SOC and mapped SOC stocks in the topmost 30 cm. We identified four causal pathways: (1) an indirect pathway representing the effect of climate on plant physiology and phenology through changes in freeze–thaw cycles and soil environment, (2) an indirect pathway representing the effect of climate on C inputs through changes in freeze–thaw cycles, soil environment and plant physiology and phenology, (3) an indirect pathway representing the effect of climate on freeze–thaw cycles, and (4) an indirect pathway representing the effect of climate on the soil environment through changes in freeze–thaw cycles. C inputs exerted the greatest control on SOC. The effect of these factors decreased with increasing soil depth. We used PLS-SEM to generate maps of SOC stocks in SFG at a 500 m resolution with a moderate accuracy. The estimated mean SOC stocks in the 0–30 cm layer reached 6.87 kg m−2, with a 95% confidence interval ranging from 6.2 to 7.5 kg m−2. Our results indicated that it is critical to consider the depth dependence of the direct and indirect effects of environmental factors when assessing the control mechanisms of SOC variations. In this work, we also demonstrated that spatially explicit SOC estimates based on timely investigations are important for assessing C stocks against the background of considerable environmental changes across the Tibetan Plateau.