Tropical paddy soil samples were collected, and the effects of different application rates of coconut shell biochar (0%, 2% and 5% (w/w)) on soil properties and microbial communities under aerobic and flooded conditions in 25 ℃ were studied by the incubation experiment. The results showed that, 1) after 35 day-incubation, 2% and 5% coconut shell biochar improved soil pH under both aerobic and flooded conditions, which increased by 20% and 39%, 31% and 32%, respectively. Under aerobic conditions, soil urease activity increased by 121% and 75%, acid phosphatase activity decreased by 10% and 49%, and alkaline phosphatase activity increased by 39% and 39%; Under flooding, soil urease activity decreased by 12% and 45%, acid phosphatase activity decreased by 3% and 14%, and alkaline phosphatase activity increased by 133% and 105%. 2) When adding 2% and 5% coconut shell biochar, Shannon index of soil bacteria and fungi decreased under aerobic conditions, but increased under flooding. Under aerobic conditions, the abundances of Proteobacteria, Gemmatimonadetes and Planctomycetes increased by 2% and 54%, 51% and 47%, 94% and 82%, respectively. Under flooding, the abundances of Acidobacteria, Firmicutes, and Bacteroidetes increased by 3% and 20%, 14% and 18%, 38% and 37%, respectively. Meanwhile, the abundance of soil Basidiomycota decreased under aerobic and flooded conditions, which decreased by 68% and 70%, 68% and 76%, respectively, and the abundances of Chytridiomycota and Rozellomycota increased under flooded conditions. The research results can provide data reference for the improvement and promotion application of coconut shell biochar in tropical paddy soil.