In order to investigate the response of continuous cropping matrix microbial community to different disinfection agents，six treatments were set up in this study，including the combination of Bacillus subtilis and Bacillus licheniformis(T1)，Hymexazol and Chlorobromoisocyanurate(T2)，Hymexazol and Copper acetate(T3)，2.2% Alcohol(T4)，Formaldehyde(T5)，and control with water treatment(CK).Based on Illumina MiSeq high-throughput sequencing platform，the effects of different treatments on the composition and diversity of matrix bacterial and fungal communities were studied.The results showed that the diversity of host bacterial and fungal communities decreased after disinfection with different agents.Compared with CK，T4 treatment significantly decreased bacterial OTU sequence，richness index(Chao 1 and Ace index)and diversity index(Shannon index)，T3～T5 treatment significantly decreased fungal OTU sequence(40.87%～47.49%)，Chao 1 index(40.58%～46.58%)and Ace index(41.16%～46.51%).The relative abundance of Chloroflexi，Firmicutes，Actinobacteri，Proteobacteria and Ascomycota reached more than 10%.Compared with CK，the relative abundance of Firmicutes，Actinobacteri and Ascomycota increased in T5 treatment，the relative abundance of tolerant bacteria Bacillaceae in the Firmicutes phylum decreased slightly，and the relative abundance of Aspergillaceae in the Ascomycota increased by 29.14%，showing as T4>T5>T3>T2>CK>T1.This study showed that different agents disinfection changed the composition of continuous substrate bacterial and fungal community，reduced the diversity of flora，with the mose obvious changes in Formaldehyde treatment.