Abstract: The role of Globally Important Agricultural Heritage Systems (GIAHS) in agro-biodiversity conservation is recently concerned. Studies have shown that the GIAHS-Qingtian rice-fish system has maintained a high diversity of rice varieties and local common carp population. The wild plant species diversity and the associated biota maintained in the GIAHS-Qingtian rice-fish system, however, are less well known. In this study, we examined plants and the associated arbuscular mycorrhizal fungi (AMF) in the field margins of the GIAHS-Qingtian rice-fish system. At the pilot site of the rice-fish system in Qingtian County, southern Zhejiang Province (120°26′–121°41′E, 27°25′–28°57′N), we investigated wild plant species diversity and collected soil samples from the rhizosphere at the field margin along a hillside with terrace fields. The α and β diversity indices of wild plants were calculated. The AMF communities in the soil samples were determined using high-throughput sequencing, and their diversity and composition were analyzed. No significant difference was found in the sample plots at different position along the slope. In the GIAHS-Qingtian rice-fish system, 109 vascular plant species belonging to 53 families in the field margin were found. Plant species α diversity (Shannon-Wiener index) was 0.74–0.84, and the β diversity (Whittaker index) was 0.67–0.77. The average AMF colonization rate of the plant species in the field margin was 6.67%–44.44%. Nine families, 14 genera, and 62 AMF species were found in soil along the field margin. The dominant AMF family was Glomeraceae, with a relative abundance of 87.29%–89.64%, and the dominant genus was Glomus (87.29%–89.64%). Carbon, nitrogen, phosphorus, and potassium contents were relatively high in the rhizospheric soil at the field margin. Correlation analysis showed that the AMF species diversity index (Shannon index) was positively correlated with the plant species diversity index (species richness). At the genus level, the AMF species diversity index (Shannon index) of Glomus was positively correlated with total soil nitrogen, available nitrogen, organic carbon, and organic matter. At the operational taxonomic unit (OTU) level, available phosphorus content had the most significant effect on the soil AMF community among the soil properties tested based on redundancy analysis. Our results showed that high plant species diversity and associated AMF were conserved in the GIAHS-Qingtian rice-fish system. These results enhance our understanding of the important role of GIAHSs in maintaining the biodiversity of agricultural ecosystems.