Protists, important components of terrestrial and aquatic ecosystems, play pivotal roles in microbial regulation, nutrient cycling and plant performance. However, understandings about how biotic and abiotic factors shape the soil protist communities remain limited. Here, we applied DNA sequencing to disentangle effects of climatic, edaphic and biotic factors on the core protist community in structuring protist communities across natural soil ecosystems. Our study revealed that soil protist community was dominated by consumers. Invertebrates and bacteria were identified as the top predictors for the biogeographic pattern of core consumers, while the core phototrophic diversity and composition were best predicted by mean annual temperature. Bacteria played the most important roles in shaping the alpha diversity and community composition of the whole protist community, followed by invertebrates. We also observed protists and bacteria had the highest robust interconnectedness within soil micro-food web. Altogether, the study indicates the importance of trophic level groups in shaping soil protist communities and implies the critical roles of trophic regulations, often underestimated, in understanding soil biota communities and soil functions in future studies. The increasing knowledge about the trophic regulations in soil microbiome is critical to interpret ecological processes and enhance soil microbial activities and functions.