Applying organic amendments enhances agroecosystem multifunctionality (EMF), yet its mechanisms via soil food-web energetics remain unclear. A field experiment was conducted on China’s Loess Plateau in a winter wheat system, comparing mineral fertilizer with straw, biochar, and liquid organic fertilizer to assess their impacts on nematode communities and EMF (plant performance and carbon, nitrogen, phosphorus cycling). Using high-throughput sequencing and energy flux modeling, we found that straw and biochar enhanced nematode diversity and co-occurrence network complexity, while liquid organic fertilizer reduced network complexity. Straw balanced fungal- and bacterial-driven energy pathways, enhancing energy flow uniformity (1.05) and EMF. However, its high C:N ratio requires mineral fertilizers to alleviate nitrogen limitations, ensuring stable bacterial energy fluxes and preventing functional trade-offs. Biochar elevated total energy flux but prioritized bacterial- and herbivore-driven pathways, reducing energy flow uniformity (0.76) and functional balance. Liquid organic fertilizer favored omnivores-predators, destabilizing lower trophic functions with minimal functional gains. Amendment properties (C:N ratio, pH) shaped nematode-mediated energy distribution, linking biodiversity to multifunctionality. Overall, straw is optimal for supporting EMF when combined with mineral fertilizers, while biochar and liquid fertilizer require tailored management to mitigate functional trade-offs. These findings advance sustainable strategies for dryland agroecosystems in the Loess Plateau region and similar environments.