Airborne microbes can survive in the atmosphere, travel intercontinental distances by air mass movement, and colonize in remote area through dry and wet deposition, thus forming a connection between oceanic, atmospheric, and terrestrial systems. However, studies linking the monsoon and bioaerosol transport are extremely rare. Here we applied high-throughput sequencing to investigate airborne microbial community succession on an island in Pearl River Estuary under summer and winter monsoon influence. The microbial communities from local potential sources (i.e., soil, leaf and surface seawater), water-soluble ions, organic carbon and elemental carbon were used to evaluate marine and terrestrial contribution. Our results revealed that airborne microbial communities underwent rapid changes during different monsoons influence (ANOSIM, P < 0.005), especially fungal aerosol. Fungal aerosols were dominant by Cladosporium, Debaryomyces, Rhodotorula, Fusarium, Aureobasidium and Candida during winter monsoon, while Coriolopsis, Ceriporia, Fomes, Phanerochaete, Trametes, Phlebia, and Antrodia were predominant fungal genera during summer monsoon. Redundant analysis showed that changes of air temperature and relative humidity caused by monsoon were the most important driven factors of airborne microbial communities in summer monsoon for airborne microbial communities. In addition, terrestrial sources were the most important contribution, especially that of soil for airborne bacteria. Some taxa were affected by atmospheric transport influenced by monsoon synoptic air mass movement.