In this experiment, we analyzed the rhizosphere fungal populations of Aquilaria sinensis (Lour.) Spreng. in different planting areas, and understood the change pattern of the rhizosphere microorganisms before and after agarwood induction, providing a reference basis for the formulation of reasonable cultivation measures for A. sinensis. High-throughput sequencing and bioinformatics methods were used to analyze the diversity and community structure of the rhizosphere soil and fungi of A. sinensis in three sample sites of Hainan province (Wenshan in Haikou, Dongguang in Lingao, and Baolun in Ledong) before and after agarwood induction, the correlation between soil physicochemical properties and fungal communities before and after agarwood induction was also clarified by redundancy analysis. The results indicated that a total of 3 697 288 ITS sequences belonging to 1 kingdom, 2 Phylum, 12 classes, 9 orders, 24 families, 55 genera, 62 species were obtained from the three planting areas. There was little variability in the fungal communities and diversity before and after agarwood induction in the sample plot, but there was significant differences in the abundance of dominant population. The Shannon diversity index of the rhizosphere soil fungi of A. sinensis before and after agarwood induction ranged from high to low: LDWJX>LDJX>LGJX>LGWJX>WSWJX>WSJX. The fungal species composition of the rhizosphere soil samples of A. sinensis was rich. There were differences in the soil fungal community composition, the relative abundance of taxonomic units and the dominant taxonomic units in the rhizosphere of A. sinensis before and after Agarwood induction in different planting areas. In terms of community structure, there were differences in the dominant populations among the three planting areas; at the Phylum level, the common dominant Phyla in the three cultivation areas were Ascomycota and Basidiomycota; at the Class level, the dominant Class in Wenshan was Dothideomycetes, In Lingao the dominant Class was Sordariomycete, In Ledong the dominant Class was Ascomycetes; at the genus level, the dominant genus in Wenshan was p__Ascomycota, in Lingao was Myrothecium, and in Ledong was c__Dothideomycetes. By correlating the physicochemical properties of the inter-rhizosphere soil with the major genera of inter-rhizosphere fungi of A. sinensis in three growing areas, it was found that soil pH, organic matter, alkaline nitrogen, total nitrogen, total phosphorus, effective phosphorus had significant effects on most of the major fungi in the inter-rhizosphere soil of A. sinensis. The results of this study are of guiding significance for the improvement of soil at the fungal level and the evaluation of soil quality of A. sinensis, and also provide a reference basis for the future fertilization strategies of A. sinensis planting areas in Hainan province.