Paulownia fortunei is a fast-growing broadleaved tree with a long history of cultivation in China. The practice of artificially inoculating this species with arbuscular mycorrhizal fungi (AMF) began in the 1980s. Artificial inoculation with AMF can greatly improve the survival rate and shorten the lengthy seedling period of P. fortunei. It is an important measure in the cultivation of strong P. fortunei seedlings. To date, however, there have been no studies on the effect of AMF on the late growth period of P. fortunei. A pure forest plantation of P. fortunei, as with other pure forest plantations, has a fast growth rate and a short rotation cycle, but its low biodiversity results in a series of problems such as soil degradation, a decline in productivity, and degradation of the ecological environment. A forest-medicinal plant intercropping ecosystem can improve the community structure of forest plantations and bring economic benefits. The present research into P. fortunei-medicinal plant intercropping ecosystems mainly focuses on the yield and economic benefits of the medicinal plants. However, AMF diversity in P. fortunei-medicinal plant intercropping ecosystems is seldom studied. We studied the colonization rate and diversity of AMF in different forestry patterns of P. fortunei of pure forest plantations and P. fortunei with medicinal plants (Polygonatum odoratum, Ophiopogon japonicus, Belamcanda chinensis) on a plain beside Poyang Lake, Jiangxi Province, China. A total of 46 operational taxonomic units (OTU) of AMF from roots of P. fortunei in four plots were obtained using the Illumina MiSeq platform. P. fortunei in pure forest plantations, P. fortunei with Polygonatum odoratum, P. fortunei with B. chinensis, and P. fortunei with O. japonicus revealed 34, 26, 24, and 20 OTUs, respectively. Unique OTUs were also found in each plot type, and the pure forest plantation of P. fortunei had the most OTUs and the most unique OTUs. The dominant AMF families in P. fortunei were Glomeraceae, Gigasporaceae, Archaeosporaceae, and Diversisporaceae. Glomeraceae was the most dominant family. There was variation in the relative abundance of the AMF from different families. Compared with the pure plantation, P. fortunei-medicinal plant intercropping ecosystems greatly changed the AMF community structure and resulted in a decrease in AMF diversity and infection rate. The Ace index and Shannon index of AMF in P. fortunei-medicinal plant intercropping ecosystems were lower than those in pure P. fortunei forest plantations, except in plots of P. fortunei with O. japonicus. However, the Shannoneven index of AMF in pure P. fortunei forest plantations was the lowest. The AMF in the Diversisporaceae were only identified in the forest plantation of P. fortunei with B. chinensis, where their relative abundance was 2.73%. These results indicated that different species in P. fortunei-medicinal plant intercropping ecosystems can change the community structure of AMF to different degrees. The effects of plant community diversity and interspecies interaction on AMF diversity and infection rate were complex. The findings of our study provide a scientific basis for further studying the ecological function and resource use of AMF in P. fortunei-medicinal plant intercropping ecosystems.