With the exacerbation of global food demand and climate change, there is an urgent need for agricultural systems to deliver multiple ecosystem functions and services. However, conventional agriculture, with its emphasis on yield maximization, has often exacerbated ecological issues such as biodiversity loss, soil degradation, and environmental pollution. Ecological intensification, grounded in nature-based solutions, aims to harmonize agricultural production with ecosystem functioning while enhancing soil multifunctionality at minimal environmental cost, thereby driving the transition of agricultural systems toward more sustainable production models. This review synthesizes the mechanisms through which ecological intensification enhances soil multifunctionality and elucidates the regulatory pathways of key management practices, including conservation tillage, diversified cropping, organic amendments, and the inoculation of beneficial organisms. Furthermore, we identified the major challenges, including the absence of a comprehensive evaluation framework for soil multifunctionality, limited understanding of trade-offs and synergies among functions, and insufficient insights into the mechanisms underlying the synergistic effects of multiple practices, and proposed targeted solutions to address these gaps. Finally, this review outlines future research priorities, emphasizing the need to establish dynamic, multi-scale research frameworks of soil multifunctionality that incorporate spatial and temporal dimensions; to deepen mechanistic understanding through theoretical and methodological innovation; and to promote regionally adaptive, context-specific management strategies through the integration of multiple ecological practices. By bridging scientific research and practical application, ecological intensification offers significant potential to simultaneously enhance agricultural productivity and ecosystem services, thereby supporting the long-term sustainability of agricultural systems.