Bioaerosols, prevalent in the atmosphere, serve as carriers for microbe transmission and can also act as Cloud Condensation Nuclei (CCN) and Ice Nuclei (IN), exerting significant influence on cloud microphysics, radiative forcing, precipitation processes, and global climate dynamics. In this study, we conducted a comprehensive study of airborne fungi from the Northwest Pacific to the Arctic Ocean. During the 9th Chinese National Arctic Research Expedition (CHINARE 2018) cruise, total suspended particulate matter (TSP) samples were collected, followed by high-throughput sequencing to determine the microbial community’s structure. Ascomycota and Basidiomycota are widespread in marine fungal aerosols along this route, with a notably higher abundance of Epicoccum and Cladosporium in fungal aerosols from the low-latitude Northwest Pacific compared to the high-latitude Arctic Ocean region. The composition of fungal communities depended on air mass transport processes and environmental factors. Long-range transport of terrestrial air masses not only enriches the abundance of fungal aerosols but also increases the relative abundance of dominant genera such as Basidiomycota, Epicoccum and Cladosporium. The knowledge gap about fungal aerosols over the Arctic route from the Northwest Pacific to the Arctic Ocean was filled in part by this work. This study deepens our understanding of how environmental factors and terrestrial air masses influence the composition and distribution of fungal community, offering valuable insights into the interconnections between marine and terrestrial ecosystems and their potential impacts on climate and atmospheric processes.