Abstract: By taking the rhizosphere soil of Passiflora edulia with different perennial root years as the research material, the effects of continuously ratooning on the structural changes of microbial communities in the rhizosphere soil of Passiflora edulia were revealed by using the ITS sequencing technology. The results showed that a total of 513420 effective sequences were measured in the rhizosphere soil of Passiflora edulia, among which 5346 Operational Taxonomic Units were annotated. The α diversity index showed that the Chao1 index, Observed species index, Simpson index and Shannon index of fungal communities in the rhizosphere soil of Passiflora edulia decreased with the year increase of continuous ratooning. The β-diversity index showed that the diversity of fungal communities in the rhizosphere soil was significantly different between the main crop in crop rotation and the continuous cropping. Through the heatmap analysis of dominant fungi at the genus level, there were some differences in the structures of fungal community in the rhizosphere soil of Passiflora edulia with continuously ratooning. With the year increase of perennial roots of Passiflora edulia, the relative abundance of Cylindrocarpon and Colletotrichum showed an increasing trend, while the relative abundance of Mortierella, Trichoderma and Plectosphaerella decreased with the year increase of perennial roots. Among them, the relative abundance of Mortierella related to beneficial fungi decreased by 81.64% with the year increase of perennial roots, while the relative abundance of Cylindrocarpon and Colletotrichum increased by 78.57% and 78.05%. Therefore, the obstacle for the continuous ratooning of Passiflora edulia might be caused by the ecological unbalance of the rhizosphere soil.