Massive spent mushroom substrate (SMS) has become an important problem that affects the ecological environment and restricts the development of mushroom industry. In the present study, SMS of Pleurotus ostreatus naturally composted for one year and two microbial agents (Bacillus subtilis BUABN-01 and Rhodotorula glutinis RG) were used for lettuce seedling. SMS with microbial inoculation twice increased the total fresh weight of lettuce by 138.90% and 57.94%, comparing with commercial control and SMS alone respectively. Microbial inoculation showed synergistic promoting effects on lettuce growth. High throughput sequencing revealed that the two microbial agents successfully colonized into SMS media, and changed the microbiota structure of SMS for promoting lettuce seedling. Heatmap and network correlation analysis showed that they can not only promote plant growth, but also stimulate beneficial microbes and inhibit potentially pathogenic microbes of plants. This work provides a feasible method and basis for the efficient utilization of SMS.