Enhancing soil organic carbon (SOC) levels via improved fertilization strategies can promote soil health and support sustainable crop production. While bacteria and fungi play a key role in SOC accumulation, the effects of soil micro-food webs that include organisms from higher trophic levels remain uncertain. We sought to narrow this knowledge gap by clarifying the associations between SOC accumulation and soil micro-food webs at the aggregate scale under long-term (18 years) fertilization treatments, which included a no-fertilizer control (Ctrl), synthetic fertilizers (NPK), and partial synthetic nitrogen replacement with pig slurry (OMNPK) or crop straw (RSDNPK). The concentration of SOC was significantly increased by fertilization following the order RSDNPK (13.1 g kg(-1)) > OMNPK (11.4 g kg(-1)) > NPK (9.1 g kg(-1)) > Ctrl (6.4 g kg(-1)). Nematodes and protists accounted for approximately 20% of all nodes in the multitrophic networks. Fertilization increased network complexity at the aggregate scale by 1-4 times across different sampling dates (P < 0.05). In all aggregate classes, the functionally important (FI) nematodes, protists, and bacterial taxa involved in soil carbon cycle had higher relative abundances under the fertilization treatments than under the Ctrl (P < 0.05). Structural equation modeling further indicated that besides soil microbes, network complexity, FI nematodes and protists were important to SOC accumulation. Compared with NPK, the key moments during which these soil biological attributes strongly regulated SOC under OMNPK and RSDNPK were delayed to late growth stages of maize. In conclusion, the increased network complexity and relative abundance of functionally important organisms from higher trophic levels of the soil micro-food webs at certain periods are vital contributors to effective SOC accumulation under fertilization regimes that include organic amendments.