Drought stress restricts plant growth and development. The flowering stage is a period of abundant microbial diversity in the rhizosphere of broomcorn millet. However, the diversity and community structure of rhizosphere fungi during the flowering stage of broomcorn millet and the response mechanism to drought stress are still unclear. In this study, two broomcorn millet varieties, ‘Hequ red millet’ (A1) and ‘Yanshu No.10′ (A2), with different drought resistances, were used as experimental materials. Using the pot water control method, drought treatment at the flowering stage was carried out, and normal watering (A1CK, A2CK) was used as the control. High-throughput sequencing technology was used to study the diversity and structural changes in rhizosphere fungi in broomcorn millet. The results show that the number of fungi OTUs in the A1, A2, A1CK and A2CK samples were 445, 481, 467 and 434, respectively, of which 331 OTUs were shared by all groups. The fungal community in the rhizosphere of broomcorn millet was mainly composed of Ascomycota and Basidiomycota. Drought treatment significantly reduced the abundance of Mortierella and significantly increased the abundance of Phoma. The abundance of Nectriaceae in the rhizosphere soil of ‘Hequ Red millet’ was significantly increased. The abundance of Pseudocercospora in the rhizosphere soil of ‘Yanshu No.10′ was higher, and the lower was Hypocreales and Nectriaceae. However, there was no significant difference in the alpha diversity of fungal communities in the four treatments, and the fungal community structure between A2 and A1CK was more similar, whereas the difference between A1 and A2CK was larger. Correlation analysis showed that drought stress had little effect on the interaction of rhizosphere fungi, and metabolic functions such as nucleotide metabolism and electron transport in rhizosphere fungi accounted for a relatively high proportion. The results show that the diversity and community structure of rhizosphere fungi were less affected by drought, which may have been due to the close interaction between species, which made the fungal community more stable under drought stress, and the difference in planting varieties may have affected the enriched rhizosphere fungal species.