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Fungi have huge biodiversity and play important roles in soil biogeochemical cycling and ecosystem services in island ecosystems. Although island biogeography has been widely studied in macroorganisms, the relationship between soil fungal diversity and area in islands is less documented. Here, we examine soil fungal communities of 18 oceanic islands belonged to two types of islands (8 general islands in Wanshan and 10 coral islands in Xisha) in South China Sea through Illumina Miseq sequencing techniques. Our results showed that soil fungal α-diversity (species richness) was significantly different among the oceanic islands, with a higher value in Wanshan than in Xisha islands. Soil fungal α-diversity was significantly affected by soil potassium and magnesium (Mg) and plant community in Wanshan islands but by soil Mg in Xisha islands. Soil fungal community composition was significantly different in Wanshan and Xisha islands and influenced by soil, plant community and spatial distance. Ecological stochasticity model showed that the fungal community assembly was mainly structured by deterministic process regardless of island types. The fungal β-diversity (community turnover), but not α-diversity was significantly increased with increasing island area. Our findings may have implications for better predicting soil fungal community dynamics in island systems and for enhancing insight into microbial biodiversity conservation.