ObjectiveTo reveal the effects of different microbial agents on quality of Lycii Fructus by comparing the differences in the contents of multiple types of chemical components in Lycii Fructus after the application of different microbial agents. MethodTaking Ningqi No. 7 as experimental material， four microbial agents， namely Peiyuan combined with Xinterui（TP group）， Trichoderma harzianum combined with Bacillus subtilis（BW group）， Genwuyou（MT group） and Junyiduo（JYD group）， were applied， and no microbial agents was used as the blank group（CK group）. Then the contents of total phenolics， total flavonoids， saccharides， amino acids， nucleosides and bases， betaine and other components in Lycii Fructus were determined by ultraviolet spectrophotometry（UV）， high performance liquid chromatography（HPLC） and ultra-high performance liquid chromatography-mass spectrometry（UHPLC-MS/MS）， and the methods such as multiple comparisons， principal component analysis（PCA） and partial least squares-discriminant analysis（PLS-DA） were used to analyze the effect of different microbial agents on the quality of Lycii Fructus. ResultMicrobial agents had different effects on chemical components of Lycii Fructus. The content of total phenolics was the highest in the TP group， and it varied significantly from the CK group（P<0.05）. The total flavonoid content was the highest in the BW group， followed by the TP group. Both polysaccharide and alduronic acid contents were the highest in the JYD group. Betaine content in the TP and BW groups were significantly higher than that in the CK group（P<0.05）. For the determined 23 kinds of amino acids， most of them were the lowest in the JYD group， and the highest in the MT group， while the nucleoside bases were higher in the MT and BW groups. It indicated that Lycii Fructus from different treatment groups could be distinguished clearly based on the determined 45 chemical components. The result of PLS-DA showed that the major differential components in each group were polysaccharides， glucose， fructose， betaine， alduronic acid， asparagine， sucrose， threonine， total flavonoids， alanine and total phenolics. The results of PCA composite scores based on the main differential components showed that composite scores of chemical components in each group were BW group>TP group>MT group>CK group>JYD group. ConclusionThe application of microbial agents of BW， TP and MT can promote the quality improvement of Lycii Fructus， and the application of JYD can promote the accumulation of polysaccharides and alduronic acid to a certain extent， but the overall effect on the quality of Lycii Fructus is not clear. This study lays the foundation for the green and healthy development of Lycii Fructus industry.