In order to understand the interaction of different microbial agents and microbial organic fertilizer,we selected susceptible wilt cucumber cultivar ‘Jinyan 4’ as the test materials.The cucumber seeds were sowed into three different seedling substrates:commodity matrix,peat-vinegar residue (volume ratio of 1∶1) and peat-vermiculite (volume ratio 1∶1),which were added “bio-organic fertilizer” (Ba),the mixed microbial agents E and the single agent B006,respectively.Then the 28 days aged seedlings were transplanted to the commodity matrix and were infected with wilt pathogen.The results showed that appropriate amount of Ba,B006 and E in all substrates could improve the cucumber seedling’s growth and chlorophyll contents.And adding microbial agents in commodity matrix was the best.Commodity matrix with 30 g Ba the plant height,stem diameter,leaf area,root volume of cucumber seedling was 1.07,1.09,1.50 and 1.30 time of CK,and the stem and leaf fresh weight,stem and leaf dry weight and root dry weight was 1.28,1.41 and 1.34 time of CK.Commodity matrix with 10 g E,the contents of Chl a,Chl b and total Chl of cucumber seedlings was 1.81,1.93 and 1.83 time of CK.Ba,B006 and E could improve the number of bacteria and actinomycetes in the bulk and rhizosphere but reduce the number of wilt pathogen.Substrate with B006,the number of bacteria and actinomycetes in bulk and rhizosphere substrate was 2.10,1.96,2.32 and 1.92 time of CK,in separately,and the number of pathogenic bacteria in bulk and rhizosphere only 19.05% and 41.00% as controls.Adding B006 and Ba wilt incidence was reduced by 37.00% and 25.00% compared to the control,respectively.The results showed that commodity matrix with 30～40 g Ba is effective in improving the quality of seedlings and adding right amount of Ba or B006 could improve plant disease resistance in growing stage.