Abstract: The fermentation residues were produced from rice straw-pig manure composting in greenhouse for CO2 fertilization. To study the effects of adding microorganisms to the fermentation residues on improvement of continuous cropping soil in greenhouse, an indoor soil cultivation experiment was conducted. The results show that after the application of fermentation residues inoculated with microorganisms, the numbers of bacteria and actinomyce are significantly increased, and the number of fungi is also increased to some extent resulting in enhancement of the bacteria/fungi ratio under the (EM+By) treatment. The activities of urease and acid phosphatase in soil are increased by NH+4-N 26.7 mg/(kgd) and phenol 127.0 mg/(kgh), respectively, and the soil pH value is increased by 1.14 unit comparing to the control treatment. At the end of the incubation period, the contents of soil available N, P and K are all significantly increased, especially the content of soil available P. In conclusion, the fermentation residues mixed with microorganisms could be utilized as a kind of biofertilizer. Application of fermentation residues inoculated with microorganisms in greenhouse could improve the quality of continuous cropping soil in the following aspects: improve the soil microbial community structure, accelerate soil nutrient transformation, increase the contents of soil available nutrients and alleviate the problem of soil acidification.