Tropical paddy soil was 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°C were studied by the incubation experiment. The results showed that (1) after 35 day-incubation, application of 2% and 5% coconut shell biochar improved soil pH under both aerobic and flooded conditions, with increases of 20% and 39%, 31% and 32%, respectively. Under aerobic conditions, soil urease increased by 121% and 75%, acid phosphatase decreased by 10% and 49%, and alkaline phosphatase increased by 39% and 39%; Under flooding, soil urease decreased by 12% and 45%, acid phosphatase decreased by 3% and 14%, and alkaline phosphatase increased by 133% and 105%. (2) When adding 2% and 5% coconut shell biochar, the Shannon index of soil bacteria and fungi decreased under aerobic conditions, but increased under flooding. Under aerobic conditions, the abundance of Proteobacteria, Gemmatimonadetes and Planctomycetes increased by 2% and 54%, 51% and 47%, 94% and 82%, respectively. Under flooding, the abundance 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, with a decrease of 68% and 70%, 68% and 76%, respectively, and the abundance 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.