This study was conducted to explore the ecological advantages in the rice-fish co-culture systems in Hani Terrace. High-throughput sequencing technique was used to analyse the bacterial diversity of water, surface soil, root soil and carp intestine (16S rDNA) between rice-carp co-culture (RC) and rice-monoculture (CK) models. The results showed that Proteobacteria, Actinomycetes, Firmicutes, Chlorobacteria, Acidobacteria, Bacteroidetes, Nitrospira and Bacteroidetes were the dominant phyla of the rice-fish co-culture systems. Compared with CK group, the relative abundance of Chlorobacteria and Firmicutes in RC surface soil significantly increased, and the significantly increased genera mainly included Anaerolineaceae_norank, Aminicenantes_p_norank, Chloroflexi_p_unclassified, Clostridium_sensu_stricto_1, Clostridium_sensu_stricto_12, Syntrophaceae_f_norank, Gemmatimonadaceae_f_norank. The relative abundance of Chlorobacteria in root soil was significantly increased in RC group compared with CK group, and the significantly increased genera included Anaerolineaceae_norank, Sideroxydans, Aminicenantes_p_norank, Chloroflexi_p_unclassified, Gemmatimonadaceae_f_norank . The dominant phyla of intestine bacterial communities in RC group were Firmicutes and Proteobacteria, and the relative abundance of Firmicutes was 58.59%. The pH, total nitrogen, ammonia-N, nitrate-N, hydrolysis nitrogen, total phosphorus, available phosphorus and soil organic carbon contents were lower in the surface soil of RC group than the CK group, and the pH, total P and available P were significantly reduced. Sobs and PD indexes of bacteria in surface and root soil of RC group were also increased, and these two indexes were significantly increased in the surface soil of RC group. In brief, the introduction of fish to rice farming ecosystems changed the physico-chemical properties and bacterial community structure of surface soils, and also affected the microbiota community structure of root soil and fish intestine to a certain extent. Our preliminary results provide microbial ecological evidences for the advantages of rice-carp co-culture over rice monoculture system.