Crop production is strongly impacted by soil nitrogen supply, which is regulated by soil micro-food webs consisting of nematodes, protists, fungi and bacteria. However, responses of soil micro-food webs to fertilization at the aggregate scale and their relationships with soil nitrogen supply and crop yield remain unclear. To address these knowledge gaps, we investigated soils subjected to typical fertilization treatments in a long-term field experiment, which included: no fertilizer control (CK); synthetic fertilizers (NPK); partial synthetic nitrogen replacement with pig slurry (OMNPK) or crop straw (RSDNPK) and incorporating biochar with synthetic fertilizers (BCNPK). The composition of different biological groups was changed significantly by fertilization, with bacteria under RSDNPK being more responsive than other groups. The co-occurrence network of the soil microfood web had more edges in microaggregates than those in large and small macroaggregates due to the significantly higher nodal degree of bacteria and fungi. On average, 76 % of the topologically important (TI) taxa in the networks were bacteria. In modules where nematodes and protists were present, 8 %-100 % of them were attributed to TI taxa while the ratio for bacteria was 3 %-7 %. Specific assemblages of functionally important (FI) taxa covering all tested biological groups at the aggregate scale were positively associated with soil labile nitrogen, related enzymes and crop yield. Random forest regression further indicates the high importance of these FI taxa to crop yield. However, less than 20 % of them were attributed to TI taxa of the networks. In summary, distinct assemblages of taxa covering multiple trophic levels regulate network topology and soil nitrogen supply + crop yield, which provides insights for targeted manipulation of soil micro-food webs through knowledgebased fertilization to harness the biological potential of cropland soils.