Sustainable agricultural intensification requires innovative approaches to simultaneously enhance productivity and mitigate environmental impacts—a challenge critical to global food security and climate change mitigation. The traditional fertilization system, with a single application of nitrogen fertilizer, while effective for crop yields, often leads to soil organic carbon (SOC) depletion, whereas green manure systems offer a dual benefit of nitrogen supply and SOC sequestration potential. However, the mechanisms by which green manure substitution enhances soil carbon sequestration (SCS) remain systematically underexplored in comparison to chemical fertilization. This review systematically examines (1) the mechanisms underlying SOC sequestration, (2) SOC losses associated with traditional fertilization practices, and (3) the theoretical foundation and practical applications of green manure as a nitrogen fertilizer substitute. We provide an in-depth analysis of the mechanisms through which green manure substitution drives SCS. Furthermore, we identify three critical areas for future investigation: (i) optimization of green manure management strategies to enhance SCS efficiency; (ii) comprehensive assessment of green manure’s ecological benefits through long-term, multi-scale studies; and (iii) evaluation of green manure’s climate change adaptation capacity and carbon sequestration potential across diverse climatic scenarios. These findings fundamentally advance our understanding of green manure’s role in sustainable agriculture by establishing its dual function as both a nitrogen source and carbon sequestration driver. In addition, these insights have immediate relevance for agricultural policy and practice, particularly in regions where soil health and carbon storage are prioritized alongside crop yield.

Green manure is widely applied in agricultural production due to its beneficial soil modification and fertilization effects. However, the mechanisms underlying the effects of green manure return methods on soil respiration (Rs) and its components remain unclear. This study aimed to investigate the effects of green manure return methods on Rs in maize fields by quantifying Rs levels. A field experiment was conducted from 2021 to 2023 in the inland river oasis irrigation area of Gansu, with five treatment conditions: tillage with a full quantity of green manure incorporated into the soil (TG), no tillage with a full quantity of green manure mulched on the soil surface (NTG), tillage with roots incorporated into the soil and above-ground green manure removed (T), no tillage with above-ground manure removed (NT), and conventional tillage and leisure (CT). The results showed that, compared with CT, the NTG treatment increased the maize grain yield while reducing the soil heterotrophic respiration rate (Rh) by 8.5–9.8% and Rs by 6.7–8.7%, but did not significantly affect the soil autotrophic respiration rate (Ra), and decreased the carbon emission efficiency (CEE) by 20.8–25.6%. The increase in the soil water content (SWC) significantly reduced Rh during all growth periods, which was the primary factor in the reduction of Rs. Additionally, the net ecosystem productivity carbon sequestration (NEP-C) of the farmland ecosystem was positive under this system, indicating that the soil acts as a carbon “sink”. Therefore, a no-tillage treatment with a full quantity of green manure mulched on the soil surface can be used as a reasonable green manure return method to reduce carbon emissions from farmland in arid oasis irrigation regions.