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<i>Siraitia grosvenorii</i>, a medicinal plant with continuous cropping, is cultivated in southern China. Changes in the soil microbial community during continuous cropping can cause soil-borne diseases in <i>S. grosvenorii</i>. This experimental study aimed to determine the differences in the arbuscular mycorrhizal fungi (AMF) community structure and root colonization in the rhizosphere soil of <i>S. grosvenorii</i> with different continuous cropping years and altitudes. We tested three altitude gradients (low, 200–300 m; middle, 500–600 m; and high, 700–800 m) and four continuous cropping years (1, 2, 3, and 5 years). AMF colonization, along with AMF spore density, and the soil physicochemical properties of <i>S. grosvenorii</i> roots at different altitudes and continuous cropping years were determined. Illumina high-throughput sequencing was used to determine the molecular diversity of AMF in the rhizosphere of <i>S. grosvenorii</i> as they exhibited a symbiotic relationship. The AMF species in the rhizosphere soil of <i>S. grosvenorii</i> included 28 species of nine genera, including <i>Glomus</i>, <i>Claroideoglomus</i>, <i>Acaulospora</i>, <i>Paraglomus, Ambispora</i>, and so on. With an increasing altitude, the AMF colonization of <i>S. grosvenorii</i> roots increased significantly (<i>p</i> < 0.01); available phosphorus (AP) content was negatively correlated with AMF colonization (<i>p</i> < 0.01). <i>Glomus</i> and <i>Paraglomus</i> were the common dominant genera in the rhizosphere soil of <i>S. grosvenorii</i> planted for 2–5 years at a low altitude and 1 year at middle and high altitudes. The average relative abundance of <i>Glomus</i> increased with increasing continuous cropping years and altitude in the low-altitude and 1-year <i>S. grosvenorii</i> areas, respectively. Slightly acidic rhizosphere soil contributed to AMF colonization and improved the richness and diversity of the AMF community. Our results showed that altitude, AP, and pH are essential factors for predicting AMF infection and community changes in the <i>S. grosvenorii</i> rhizosphere. Here, Illumina high-throughput sequencing was used to study the species resources and community composition of mycorrhizal fungi in <i>S. grosvenorii</i> in the hilly areas of Guangxi, China. This study provides a theoretical basis for the application and practice of mycorrhizal fungi including the isolation and screening of dominant strains, inoculation of mycorrhizal fungi, and exploration of the effects of mycorrhizal fungi on the growth and active ingredients of medicinal plants.