In order to investigate the differences in the composition of water flora and intestinal flora of penaeus monodon caused by different culture modes，the experiment was carried out in low-salt soil ponds （salinity： 8.3‰，hereinafter referred to as the low-salt soil pond group）， low-salt intensive pond culture （salinity：7.8‰，hereinafter referred to as the low-salt intensive pond group）， and high-salt intensive pond （salinity： 23.4‰， hereinafter referred to as the high-salt group）. High throughput sequencing technology was used to study the structure and diversity of penaeus monodon aquaculture water microbiota and intestinal microbiota at 40， 80， and 120 days respectively. The structure and diversity of water flora and intestinal flora were investigated. The results showed that there were significant differences in the changes of culture water and intestinal flora in different stages of shrimp in different culture modes（P<0.05）. There were 1 005，1 443， and 1 282 microbial species detected in the water column of low-salt soil pond， low-salt intensive pond and high-salt intensive pond， belonging to 26， 29， and 29 phyla respectively； 1 521， 877， and 451 microbial species were detected in the intestines，belonging to 38， 23， and 21 phyla respectively. The dominant phyla in the water flora of different models of penaeus monodon culture were Phylum Anaplasma， Phylum Actinomycetes， Phylum Anaplasma， Phylum Cyanobacteria and Phylum Desulfovibrio；the dominant phyla in the intestines were Phylum Thicket， Phylum Anaplasma， Phylum Actinomycetes， Phylum Anaplasma and Phylum Cyanobacteria. The Rhodobacteraceae belonging to the phylum Anaplasma were dominant in both the water column and the gut， while the lactobacillaceae belonging to the phylum Thick-walled were dominant only in the gut of penaeus monodon； in the gut of penaeus monodon， the Rhodobacteraceae were the main dominant bacteria in the early stages of culture， while the lactobacillus and weisseria spp. showed absolute dominance in the gut in the later stages of culture. The results showed that there were significant differences in the water flora and intestinal microflora of penaeus monodon in different cultural modes. The relative abundance of Rhodobacteraceae and Lactobacillus in high salt high position ponds was significantly higher than that in low salt soil ponds and low salt high position ponds. Some bacteria in lactobacillus and weisseria genera may be potential probiotics during the Penaeus monodon culturing process.