The importance of soil macropores has been wildly recognized, which permit the rapid flow of water through soils. However, few studies have focused on the soil macropores of different alpine meadow soil in cold environments in the Qinghai-Tibet Plateau. This study aims to use computed tomography to quantify the soil macropore and root architecture of Meadow swamp soil, Sub-alpine shrub meadow soil, Sub-alpine grassland meadow soil and Sub-alpine meadow soil in the Qinghai Lake Watershed of the northeastern Qinghai-Tibet Plateau. A total of twelve soil cores (0–50 cm deep) were collected at four typical soil types under alpine meadow, with three replicates. At each site, the collected cores were scanned using the X-ray 3D microscope (Nano Voxel-2000, Sanying Precision Instruments Co., Ltd.). The soil macropores and root architecture of the soil cores were explored using the X-ray computed tomography method. The results indicated that the Meadow swamp soil and Sub-alpine shrub meadow soil had higher macropores than Sub-alpine grassland meadow soil and Sub-alpine meadow soil. Sub-alpine grassland meadow soil and Sub-alpine meadow soil had macropores that were mainly concentrated in the 0–100-mm soil depth. Moreover, macropore networks of Meadow swamp soil and Sub-alpine shrub meadow soil were more convoluted and continuous than those of Sub-alpine grassland meadow soil and Sub-alpine meadow soil. Root density was greater in the Meadow swamp soil and Sub-alpine shrub meadow soil than those in the Sub-alpine meadow soil and Sub-alpine grassland meadow soil. The soil macropore architecture with a high continuity could facilitate greater water flow to deeper soil layers in the Meadow swamp soil and Sub-alpine shrub meadow soil than in the Sub-alpine grassland meadow soil and Sub-alpine meadow soil. Root density, root node density, length density and surface area density and branch density were important parameters influencing soil macropore. Soil macropore length density was significantly and positively correlated to soil near saturated hydraulic conductivity K (10). Soil water status and alpine shrub root induce greater macroporosity of Meadow swamp soil and Sub-alpine shrub meadow soil than Sub-alpine grassland meadow soil and Sub-alpine meadow soil, and thus present a greater likelihood of larger macropores.