[Objective] The response of microbial biomass carbon and nitrogen in greenhouse soil to the addition of fungal residue was studied in order to provide theoretical basis and technical support for the sustainable development of greenhouse production. [Methods] Field experiments were conducted in Shenxian County, Shandong Province, with six organic fertilizer treatments which application of chicken manure (CON) and five application rate of fungal residue (FR), to examine the effects of fungal residue on organic carbon (SOC), total nitrogen (TN), microbial biomass carbon (MBC) and nitrogen (MBN) in greenhouse soil. [Results] Compared with CON, the application of 5 fungal residue treatments (The usage of bacteria residues was 15, 30, 45, 60 and 75 t/hm² respectively) increased SOC by 12.0%, 11.2%, 21.6%, 33.1% and 31.7%, respectively, and increased TN by 3.1%, 6.3%, 19.9%, 29.4% and 26.4%, respectively. The later four treatments increased the MBC (16.1%, 19.9%, 36.8% and 50.7%) and the MBN (3.3%, 37.7%, 40.4% and 60.9%), compared to the CON treatment. There were significant positive correlations between MBC, MBN and SOC, TN. [Conclusion] The application of fungal residue could increase the contents of SOC, TN, MBC and MBN, and the content of MBC and MBN increased with the increase of fungal residue to the field. As a result, the appropriate application of fungal residue could improve the soil microbial activity and soil fertility in greenhouse soil.