Abstract: Taking Glycyrrhiza uralensis as the test material, the green house paitition test was curried ont.Set up no application microbial fertilizer as control treatment（CK）,and applying Purpureocillium lilacinum（PL）,Bacillus subtilis（BS）,Trichoderma harzianum（TH） and tis compound treatment（MX）,which carried out to explore the effects of different microbial fertilizers on photosynthetic pigments, chlorophyll fluorescence, PSⅡ photochemical characteristics, flavonoid synthesis and soil microbial quantity of Glycyrrhiza uralensis,in order to provide reference for microbial fertilizer of Glycyrrhiza uralensis.The results showed that compared with CK treatment, microbial fertilizer treatments（PL,BS,TH,MX） increased the content of photosynthetic pigments（chlorophyll a, chlorophyll b, carotenoids）,enhanced chlorophyll fluorescence(Fv/Fm, qP, Φ_PSⅡ),and reduced the characteristics of PSⅡ photochemical loss characteristics（φDo, φPo, Ro, Ψo）,the flavonoid components（glycyrrhizin, glycyrrhisoflavone, licorice dihydroflavone, licorice chalcone） were increased, and the overall performance of each treatment was CK＜PL,TH＜MX,BS.Furthermore, microbial fertilizer also increased the number of soil bacteria, ammonia-oxidizing bacteria, actinomycetes and nitrogen-fixing bacteria, and had no significant effect on fungi.In summary, the application of microbial fertilizer could improve the efficiency of photosynthesis and the number of soil microorganisms, and increase the content of flavonoids, and the application of Bacillus subtilis fertilizer was the best treatment.