Membrane-covered systems can effectively optimize composting process and decrease gas emissions during composting. To explore the effects of the membrane-covered system on composting with and without microbial inoculation, four treatments were conducted: a control without membrane and without microbial inoculation (CK), membrane-covered composting (MCK), composting with microbial inoculation (I), and membrane-covered composting with microbial inoculation (MI). The results showed that membrane-covered systems (MCK, MI) reduced the emissions of NH3, CH4, and CO2 in composting. Compared to I, MI decreased the degradation of cellulose and hemicellulose but significantly increased the degradation of lignin by 88.3% (P < 0.05), improved the humification degree significantly by 71.6%. Moreover, principal coordinate analysis and redundancy analysis indicated that membrane-covered systems altered the microbial succession especially in MI. A random forest analysis demonstrated that the relative abundance of bacterial and fungal genera associated with the humification degree were changed in membrane-covered systems during composting. Therefore, the membrane-covered composting with microbial inoculation may be an efficient and promising strategy for improving compost quality by promoting humification and altering microbial communities.