Continuing permafrost degradation is increasing the risk of mercury (Hg) exposure in the permafrost regions on the Qinghai-Tibetan Plateau (QTP), but related studies are still limited, especially the ones on the detailed Hg migration processes in permafrost. The vertical distribution characteristics of soil Hg were investigated in three ecosystems in the Beiluhe area on the QTP, and its influencing factors and formation mechanism were investigated. The results indicate that the total soil mercury (THg) concentration in the Beiluhe area remains at an extremely low level (6.33 ± 2.45 ng/g). In the vertical profile, the THg concentration of the shallow soil layer (0–50 cm) (5.96 ± 2.22 ng/g) is significantly lower than that of the deep layer (50–400 cm) (7.44 ± 2.71 ng/g) (p < 0.05). Within the upper 50 cm, the THg concentration decreases with soil depth, and the peak THg concentration occurs at 100–300 cm on the entire profile. Although the THg concentration is slightly affected by the organic matter in the shallow soil layer, in general, the soil parent material is the dominant factor affecting the THg concentration. Intense weathering results in a low THg concentration in the shallow soil layer because the soil Hg is carried downward with the soil moisture. To a certain depth, the impermeable frozen soil layer intercepts the flow of the soil Hg, and it forms a Hg enrichment layer. This paper presents the distinctive pattern of the soil Hg distribution in the permafrost regions of the QTP.