Long-term fertilization shapes the size and community composition of the soil food web by altering resource quantity and quality. Previous studies have examined specific components; however, comprehensive effects on the entire food web and underlying mechanisms remain unclear. In this study, a 30-year experiment in a rice–wheat cropping system was conducted to assess the effects of chemical fertilizer (NPK), manure (M), and their combination (NPKM), with unfertilized soil as the control. Biomass or abundance across key taxonomic and functional groups - including microorganisms, protozoa, nematodes, mites, collembolans, enchytraeids, and earthworms - was measured, and nematode ecological indices were calculated to evaluate bottom-up and top-down regulatory influences. Results showed that long-term fertilization increased resource inputs, thereby enhancing most functional groups. M and NPKM outperformed NPK across most groups, with relative increases compared to NPK ranging from 20.69 to 972.52% under M (average: 241.62%) and from 26.55 to 792.30% under NPKM (average: 189.02%). However, differences between M and NPKM were not significant, as high soil fertility diminished the divergence in their effects. Strong evidence for bottom-up control was observed, supported by positive correlations among functional groups and by increases in the enrichment index (51.27 and 28.49%) and enrichment footprint (11.80 and 47.17%) under M and NPKM relative to NPK. Partial least squares path modeling further confirmed that bottom-up forces predominantly determined food web structure and biomass. These findings indicate that sustained organic inputs, particularly when integrated with mineral fertilizers, effectively enhance soil food web complexity and size primarily through bottom-up regulatory mechanisms.