Livestock grazing can affect both above- and below-ground communities, however, the effects of grazing intensity on vertical distribution of root traits and their associations with belowground food webs are still unclear. Based on a 5-year grazing intensity experiment (i.e., no grazing, moderate grazing and heavy grazing) in a Tibetan plateau meadow, we investigated how grazing-induced changes in root traits affected soil biota (microbes and nematodes) from the surface (0–10 cm) and subsurface soils (10–20 cm). Our results showed that moderate grazing increased nematode abundance and structure complexity of the soil micro-food webs compared to no and heavy grazing, and predominantly increased herbivores and fungivores regardless of soil layers. Shifts in herbivores and fungivores were mainly driven by root quantity and quality, emphasizing the stronger bottom-up effects on the lower trophic levels of nematodes. Grazing decreased the number of omnivores-predators in the surface soil compared to no grazing, which therefore weakened predation pressure on soil nematodes lower in the trophic structure, including root herbivores, while that effect was far less pronounced in the subsurface soil. Our study demonstrated that changes in root quantity and quality were highly associated with the complexity of the soil micro-food webs under grazing scenarios. These findings warranted the ideas that combined aboveground herbivore-root-soil micro-food webs as an ecological holo is essential for sustainable management of grassland.