Composting offers an eco-friendly approach, converting organic solid waste into valuable soil enhancer products. Three experimental treatments were designed to explore the microbial mechanisms influencing lignocellulose loss in rice straw composting: CK (the control), B4 (inoculated with Bacillus subtilis), and Z1 (inoculated with Aspergillus fumigatus). The results showed significant increases in carboxymethyl cellulase, cellobiohydrolase, laccase, and xylanase activities during B4 and Z1composting. However, lignin peroxidase and manganese peroxidase were not significantly affected, and β-glucosidase was inhibited. Additionally, microbial inoculation stimulated lignin loss, with B4 and Z1 composting increasing degradation by 14.42% and 16.29%, respectively, compared to the CK. Simultaneously, humic substance content increased as microbial inoculation inhibited β-glucosidase, causing cellobiose to accumulate and divert into a pathway that forms humic substances. The random forest model showed that Symmetrospora and Phaeosphaeria significantly boosted lignocellulose loss in B4 and Z1 composting by promoting fungi functional aggregation, thus accelerating the degradation and transformation process. This study explored the microbial mechanism of lignocellulose loss and provided new insights into lignocellulose conversion and carbon fixation. Display omitted •The functional aggregation of fungi was promoted by inoculation.•The microbial linkage mechanism behind lignocellulose loss was proposed.•β-Glucosidase was inhibited leading to cellobios entering the bypass pathway.•Symmetrospora and Phaeosphaeria make great contributions to lignocellulose loss.•The linkage mechanism was initiated by inoculation of functional microbes.