The aim of the present study was to investigate the effect of wound location on the fungal communities and volatile distribution of agarwood in
Aquilaria sinensis
. Two-dimensional gas chromatography with high-resolution time-of-flight mass spectrometry revealed 60 compounds from the NIST library, including 25 sesquiterpenes, seven monoterpenes, two diterpenes, nine aromatics, nine alkanes and eight others. Of five agarwood types, Types IV and II contained the greatest number and concentration of sesquiterpenes, respectively. The fungal communities of the agarwood were dominated by the phylum Ascomycota and were significantly affected by the type of wound tissue. Community richness indices (observed species, Chao1, PD whole tree, ACE indices) indicated that Types I and IV harboured the most and least species-rich fungal communities, and the fungal communities of Types V, I, III and IV/II were dominated by
Lasiodiplodia
,
Hydnellum
,
Phaeoisaria
and
Ophiocordyceps
species, respectively. Correlations between fungal species and agarwood components revealed that the chemical properties of
A. sinensis
were associated with fungal diversity. More specifically, the dominant fungal genera of Types V, I and III (
Lasiodiplodia
,
Hydnellum
and
Phaeoisaria
, respectively) were strongly correlated with specific terpenoid compounds. The finding that wound location affects the fungal communities and volatile distribution of agarwood provides insight into the formation of distinct agarwood types.