The alpine regions are characterized by frequent freeze-thaw cycles, which influence the soil structure remarkably. However, the effects of freeze-thaw cycles on the soil macropore structure and its implications on the formation of hummocks are not well understood. This study aims to quantify the soil macropores of hummocks and the effects of freeze-thaw cycles on soil macropores to reveal its implications on the formation of hummocks in alpine meadows. A total of nine intact soil columns (0–50 cm deep) were excavated from the alpine meadows. Three replicates were collected from the hummocks and three were collected from the interhummocks, and they were scanned by X-ray computed tomography (CT). Another three replicates were excavated from the adjacent non-hummock alpine meadows, which were subjected to successive freeze-thaw cycles (0, 1, 3, and 6) and then scanned using X-ray CT. Soil macropore network of hummocks was more extensive and continuous than that of the interhummocks. The volumetric distribution of soil macropores in hummocks was multiple, while soil macropores of the interhummocks intensively fell in the volume range of 0–400 mm3. The soil macroporosity, macropore number density, surface area density, length density, node density, branch density, and mean macropore size of the hummocks were several times higher than those of the interhummocks. These soil macropore parameters showed a decrease after the first and third freeze-thaw cycle and later increased through the next three cycles. Soil macropores with volume > 1000 mm3 transformed into smaller ones (600–1000 mm3) during the freeze-thaw process. The soil macropore patterns of hummocks and interhummocks differed distinctly. Soil macropores responded significantly to freeze-thaw cycles. The effects of freeze-thaw cycles on the macropore number and size were more significant than on the morphology in alpine meadows. Hummock formation is closely related to the soil macropores during the freeze-thaw cycles, and the soil moisture played a crucial role in the hummock formation process.