The areca nut (Areca catechu L.) and pandan (Pandanus amaryllifolius Roxb.) intercropping cultivation system has been widely practiced to improve economic benefits and achieve the development of sustainable agriculture in Hainan Province, China. However, there is a lack of research on the relationships among soil properties, soil enzyme activities, and microbes in this cultivation system. Therefore, a random block field experiment of pandan intercropped with areca nut was established to investigate the effects of environmental factors on the diversity and functions of soil microbial communities in Lingshui county, Hainan Province. The diversity and composition of soil microbial communities under different cropping modes were compared using Illumina sequencing of 16S rRNA (bacteria) and ITS-1 rRNA (fungi) genes, and FAPROTAX and FUNGuild were used to analyze and predict the bacteria and fungi community functions, respectively. Correlation analysis and redundancy analysis were used to explore the responses of soil microbial communities to soil environmental factors. The results showed that the bacterial community was more sensitive to the areca nut and pandan intercropping system than the fungal community. The functional predictions of fungal microbial communities by FAPROTAX and FUNGuild indicated that chemoheterotrophy, aerobic chemoheterotrophy, and soil saprotroph were the most dominant functional communities. The intercropping of pandan in the areca nut plantation significantly enhanced the soil bacterial Ace and Chao indices by reducing the soil organic carbon (SOC) and total phosphorus (TP) content. In the intercropping system, urease (UE) and acid phosphatase were the key factors regulating the soil microbial community abundance. The dominant bacterial and fungal phyla, such as Firmicutes, Methylomirabilota, Proteobacteria, Actinobacteria, Chloroflexi, Verrucomicrobia, and Ascomycota significantly responded to the change in planting modes. Soil properties, such as UE, total nitrogen, and SOC had a significant stimulating effect on Proteobacteria, Chloroflexi, and Ascomycota. In summary, soil bacteria responded more significantly to the change in cropping modes than soil fungi and better reflected the changes in soil environmental factors, suggesting that intercropping with pandan positively affects soil microbial homeostasis in the long-term areca nut plantation.