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Background: Agroforestry is a promising approach for sustainable agriculture due efficient resource cycling and improved soil fertility. Bombax ceiba (Malvaceae), a tall tree with red flowers blooming in spring, is traditionally planted in rice fields in tropical Asia. However, the role of B. ceiba in the agroforestry systems remains unexplored. Methods: We collected 81 soil samples at different distances to B. ceiba (0 m (D0), 1 m (D1), and 5 m (D5)) at a typical B. ceiba-rice agroforestry system in Hainan Island (south China) during three reproductive stages of rice- booting, heading and maturity. We assessed spatiotemporal variations of soil nutrient properties (by a soil nutrient analyzer (YT-TRX03)), and soil bacterial and fungal communities (by sequencing 16S rRNA gene and internal transcribed spacer (ITS) region, respectively). Results: B. ceiba improved the soil nutrient conditions in a rice field, particularly the availability of potassium and soil organic matter. Soil microbial communities were significantly affected by the distances to B. ceiba and the reproductive stages of rice. Available potassium was the principal driver of soil bacterial diversity and structure. In contrast, fungal diversity was negatively correlated with total nitrogen, while soil organic matter was the main factor shaping fungal community structure. Conclusions. Our results show that B. ceiba has positive impacts on abiotic traits of rice-growing soils. B. ceiba can change soil microbial community structure, however, the principal soil driver varied according to microbial taxa. These findings support the ecological basis of traditional agroforestry systems prevalent in tropical Asia. [ABSTRACT FROM AUTHOR]