Eucalyptus plantations are controversial because of its complexed impacts on environments. Arbuscular mycorrhizal (AM) fungi in soil provide important ecological functions such as enhancing soil nutrient transportation and plant stress tolerance via symbiosis. Until recently, the influence of massive Eucalyptus planting on soil microbial communities, especially the AM fungi is yet to be investigated. Herein, we investigated into these effects by comparing the diversity and taxonomic composition of AM fungal community in soil between the secondary forest and Eucalyptus forests which involved two-, five-, and ten-year's plantations. Our results provided evidence that the practices of Eucalyptus plantations significantly changed soil properties (P < 0.05), e.g., the soil pH and soil organic carbon significantly decreased in the two- and ten-year's soil samples relative to the secondary forest. Importantly, spore density of AM fungi in soil declined by the Eucalyptus plantations, with the lowest level being observed in the five-year plantation. Species richness of AM fungi inclined to decrease within five years of Eucalyptus plantation, but recovered to a contain extent after ten years. In contrast, AM infection rate on the roots of Eucalyptus reached to the highest and lowest level in the five-year and ten-year plantation, respectively. Further, the composition and structure of AM fungi shifted significantly by Eucalyptus plantations. Noticeably, the dominant species Funneliformis geosporus and Septoglomus deserticola significantly decreased and increased in the two- and ten-year Eucalyptus plantations, respectively. Lastly, our redundancy analysis indicated that soil pH largely promoted the variation of the AM fungal community (explanation rate: 89.88%). Collectively, our study revealed the shifts of AM fungi in the soil of the secondary forest after the practices of Eucalyptus plantations, which is necessary to shed light onto the strategies of environment restoration in Eucalyptus plantations.