Ecosystem multifunctionality (EMF) serves as an integrated indicator of nutrient cycling, water regulation, and productivity in agroecosystems, exhibiting high sensitivity to cover crop management. Soil biodiversity underpins essential ecosystem services essential to human well-being. However, cover cropping exerts complex effects on soil abiotic conditions and the diversity of soil microbes, nematodes, and earthworms, introducing uncertainty regarding its regulation of EMF. This study investigated how ryegrass (Lolium perenne L.) cover cropping duration influences EMF in apple orchards on the eastern Loess Plateau. Compared to clean tillage, ryegrass cover cropping significantly enhanced soil carbon, nitrogen, and phosphorus cycling functions, productivity, and overall EMF. These benefits followed a unimodal trajectory, peaking at approximately 5 years post-establishment before declining. Crucially, multitrophic biodiversity exerted a stronger influence on EMF than diversity within any single trophic level. Collectively, soil microbes, nematodes, and earthworms explained 74% of the variation in EMF, with smaller, lower-trophic organisms contributing more substantially than larger, higher-trophic organisms. Structural equation modeling identified soil organic carbon and available nitrogen, rather than soil pH, as the primary abiotic drivers of EMF under ryegrass cover cropping. Our findings demonstrate that cover cropping-induced nutrient changes cascade through soil food webs, shaping multitrophic diversity and thereby regulating EMF. These observations highlight that maintaining cover crops for approximately 5 years optimizes EMF, providing targeted guidance for sustainable apple orchard management on the eastern Loess Plateau.