Soils in the Qinghai‐Tibet Plateau are young in terms of development and form a thin, skeletal soil layer because the gravel parent materials are glaciofluvial deposit, eluvium, and fluvial sediment, which are extremely sensitive to global climate change. The lack of understanding of soil organic matter (SOM) transformation processes in this region hinders the prediction of SOM stocks under future climate conditions. In this study, SOM transformation processes were investigated by density groupings and pyrolysis‐gas chromatography/tandem‐mass spectrometry (Py‐GC–MS/MS) in five alpine ecosystems: alpine desert, alpine grassland, alpine meadow, alpine wetland, and alpine forest. The roles of microbial community in different density fractions were elucidated. Soil samples were separated into three fractions with NaI solution: labile fraction (FL; ρ ≤ 1.6 g/cm3), moderate fraction (FM; 1.6 < ρ < 2.25 g/cm3), and recalcitrant fraction (FR; ρ ≥ 2.25 g/cm3). The following results were obtained. (1) The ratios of different fractions (FM/FL, FR/FM, and FR/FL) indicated the transformation processes of SOM, and ratios less than 1 represented degradation. The transformation processes were similar in alpine grassland and meadow and were similar in alpine desert, wetland, and forest but differed from each other. (2) Fungi preferred to degrade plant detritus, which mainly affected FL, whereas bacteria chiefly affected FM. (3) Precipitation altered vegetation type and soil pH, thus affecting communities and microorganism activities and resulting in the above differences. These findings highlight the importance of understanding the limited transformation processes of SOM in ecosystems to predict the impact of climate change on SOM preservation.