Background: Fly ash is the product of coal combustion, and a large amount of fly ash accumulation is of great harm to the environment. The yellow horn (Xanthoceras sorbifolia Bunge) is a unique edible oil tree species in China. Yellow horn has developed root system and can survive in soil contaminated with heavy metals. Thus, it could be used for phytoremediation in fly ash. Results: In this study, high-throughput 16S rRNA and ITS rDNA gene Illumina sequencing technology was used to analyze the microbial community diversity in fly ash before (CK group) and after (S group) planting yellow horn. The abundance and diversity of microorganisms in fly ash were changed by planting yellow horn. The dominant bacterial phyla: Proteobacteria (CK-24% vs S-42%), Firmicutes (CK-23% vs S-10%), Actinobacteria (CK-15% vs S-11%). The dominant phyla in fungi: Ascomycota (72% for CK, 69% for S), Mortierellomycota (4% for CK, 3% for S).Some beneficial bacteria that could degrade heavy metals increased in proportion, including Betaproteobacteriales (4% for CK vs 10% for S group), Burkholderiacae (1% for CK vs 6% for S groups), Nitrospirae (0.3% for CK vs 0.8% for S groups), Rhizobiales (3% for CK vs 6% for S groups) and Sphingomonadaceae (2% for CK vs 4% for S groups). Conclusion: These results indicate that the planting of yellow horn can increase the abundance of heavy metal-degrading bacteria in rhizosphere fly ash, which is of great significance for the biological remediation of fly ash.