To improve the application effect of EM microbial agent in spent mushroom substrate composting, accelerate the process of decomposition and improve the quality of the compost, an enhanced EM microbial agent was prepared by adding the cellulase and xylanase-producting strain Aspergillus niger SNH-7 and the protease-producing strain Bacillus subtilis SNK-103 to the common EM microbial agent, and its effect on spent mushroom substrate composting was studied. Results showed that the microbial metabolism was more vigorous during composting by inoculating the enhanced EM microbial agents, comparing with common EM microbial agents. The physical and chemical indexes such as temperature, pH, EC, total organic carbon, soluble organic carbon, total nitrogen, ammonium nitrogen, nitrate nitrogen, C/N, humic acid and fulvic acid content increased or decreased more greatly, which meant that the maturation process was accelerated. The GI of the finished compost increased, C/N decreased, and the contents of total nitrogen, nitrate nitrogen, total humic acid and free humic acid increased, which indicated that the compost had better biological safety and higher fertilizer efficiency. All these indicated that supplementation of high-yield strains of cellulase, xylanase and protease in EM microbial agent could accelerate the composting process of spent mushroom substrate and improve the composting quality by strengthening its ability to degrade cellulose, lignin and protein under no excipients, high C/N, and low pH.