Composting is widely used for agricultural waste management, and the composting method significantly influences composting processes. This study compared static composting (SC), turning composting (TC), forced aeration composting (AC), and membrane-covered forced aeration composting (MAC) to evaluate which method is more effective for mitigating carbon emissions and promoting humification. Compared to the other methods, MAC shortened the composting period and reduced cumulative CH 4 emissions by 53.4%–99.7% and cumulative CO 2 emissions by 25.7%–66.2%. Moreover, MAC promoted the formation and transformation of humic precursors, achieving the highest degree of humification among the methods. Microbial–physicochemical association networks suggested that MAC had more microorganisms associated with humic-precursor-related processes than with carbon-emission-related processes. Microbial co-occurrence networks further revealed that MAC enhanced microbial cooperation, particularly bacterial–fungal interactions, which played a critical role in humification. Notably, MAC increased the relative abundance of bacterial pathways associated with substrate metabolism in the early stage and enriched pathways for secondary metabolite biosynthesis in the late stage, while shifting the fungal community toward saprotroph dominance. Overall, by combining a parallel comparison of composting methods with the elucidation of the underlying microbial mechanisms, this study reinforced the application potential of MAC. • Membrane-covered forced aeration composting (MAC) reduced carbon emissions. • MAC resulted in the highest degree of polymerization (DP = 1.91). • More microorganisms processed humus precursors than carbon emissions in MAC. • MAC enhanced microbial cooperation intra- and inter-domain. • MAC enhanced humification-related bacterial metabolic pathways.