Alpine meadow occupies ~46.7 % of the grassland area and stores more than 60 % of the soil organic carbon (SOC) in the Qinghai-Tibet Plateau, with 3.19 Pg C in the top 30 cm. Parent material can highly influence SOC stocks via various mineral components with divergent adsorption abilities. However, previous studies mainly concentrated on the relation between SOC and parent material in temperate and tropical forest ecosystems, evidences from different environments are needed to gain a holistic understanding. In this study, we explored how the functional distinct SOC fractions (the particulate (POC), mineral-associated (MAOC), and hot-water extractable carbon (HWEOC)) vary among four types of parent materials (monzonitic granite (MG), slate (SL), muscovite schist (SH), and diorite (DI)) by measurements from 16 sites on the Qinghai-Tibet Plateau. We also assessed the plant and geochemical factors in controlling the divergent SOC fractions. We found that MAOC and HWEOC vary strongly, while POC remain stable among parent materials due to sufficient plant input and slow decompositions rate. Moreover, our results revealed that geochemical factors exert dominant controls on each SOC fraction, with soil pH and texture showing a significant influence. Soils developed from the SL displayed the highest MAOC and HWEOC compared with that formed on the other three parent materials due to finer soil texture as well as relative high multivalent Ca and Mg. Furthermore, root traits increased its control on SOC fractions in relatively deeper soil depth (10–30 cm). Taken together, these results provided evidence of the key role of parent material in controlling the divergent SOC fractions in the less weathered alpine regions, emphasizing that parent material and soil geochemistry should be adequately considered in the biogeochemical and Earth system models.