Soil microbes drive nutrient cycle and strongly affect the fluxes of greenhouse gases (GHGs) globally. However, the mechanisms through which the key functional guilds regulate GHG fluxes from cropland remain unclear, especially those involving organisms at higher trophic levels of the soil micro-food webs. Therefore, the responses of key functional guilds to fertilization strategies and their contributions to the fluxes of dominant GHG were estimated to improve our mechanistic understanding. Typical fertilization regimes across the country were included in a long-term field experiment: regular synthetic fertilizers (NPK), partial synthetic nitrogen replacement with pig slurry (OMNPK) and crop straw (RSDNPK) plus a nil fertilizer control (Ctrl). The soil was a net sink of CH4, while fertilization treatments increased the fluxes of N2O and CO2. The cumulative N2O and CO2 emissions followed the order of RSDNPK > OMNPK approximate to NPK > Ctrl. Among the three GHGs, CO2 was the dominant one due to its high quantity and showed strong correlations with five soil labile and stable organic carbon and nitrogen fractions. The key functional guilds that strongly correlated with CO2 fluxes at the aggregate scale were composed of not only soil microbes, but also protists (14-19 %) and nematodes (3-4 %). Fertilization with organic amendments (OMNPK and RSDNPK) significantly changed the composition of the key functional guilds, which, along with key soil parameters, explained 26-35 % of the variation in CO2 fluxes. Protists were ranked as the 1st or 2nd most important biological group in determining the composition of the key functional guilds in all aggregate classes. Conclusively, soil biological groups at higher trophic levels, particularly protists, can serve as the important driver of GHG emissions. Manipulating their activities through targeted fertilization offers an alternative to mitigate the climate impacts of crop production.