The application of animal manure containing antibiotic residues to farmlands as an organic fertilizer causes a long-term potential threat to the ecological environment of farmland. This study analyzed the effects of abating typical antibiotics and resistance genes (ARGs) applied with pig manure on farmland soil as well as on soil ecosystem multifunctionality (EMF) and its influencing factor. The results showed that Lolium multiflorum exhibited significantly stronger abatement of typical antibiotics and ARGs when combined with biochar than when used alone (p < 0.05). The dissipation of antibiotics significantly enhanced the soil functions (respiratory, ammonification, and nitrification activities) (p < 0.05). A structural equation model was established to explore the effects of abating antibiotics and ARGs in different treatment systems on soil EMF. The treatment of plant roots with ryegrass alone and in combination with biochar exerted direct positive effects on the physical structure and EMF (p < 0.001). The improvement in soil physical structure directly promoted the abatement of antibiotics and ARGs (p < 0.01). Soil pH and trace elements exerted weaker effects on antibiotics and ARGs after the application of biochar. Plant roots were the most important factor in promoting the EMF of soil containing antibiotics and ARGs.