The early development of plants plays a crucial role in shaping the microbial community within the rhizosphere soil. This study aims to investigate the impact of Panax notoginseng seedling strips on the fungal community structure in red loam soil. Rhizosphere soil (HA) samples were collected from healthy P. notoginseng seedling strips, while non-rhizosphere soil (CK) samples were obtained without any P. notoginseng seedlings. High-throughput sequencing was performed on these samples using ITS rRNA. The results showed that the number of orders, families, genera and species in non-rhizosphere soil was significantly higher than those in the rhizosphere soil of P. notoginseng seedlings (P<0.05). At the taxonomic level, Ascomycota accounted for a major proportion of fungal communities (CK 50.84%, HA 78.12%), followed by k__Fungi_Unclassified (CK 17.96%, HA 5.09) and Basidiomycota (CK 16.50%，HA 2.53%). Diversity analysis revealed significantly higher values for ace, chao1, Shannon and Simpson indices in non-rhizosphere soil compared to rhizosphere soil (P<0.05). PCoA analysis demonstrated a significant difference in fungal community structure between rhizosphere and non-rhizosphere soils with low community similarity (R²=0.6776，P=0.005). Enrichment analysis identified several fungi groups enriched in non-rhizosphere soil including Basidiomycota, Dothideomycetes, and Eurotiomycetes; whereas only Ascomycota, Sordariomycetes and Xylariales were significantly enriched in rhizosphere soil including Trichoderma, Scopulariopsis and Monographella. Notably, Trichoderma (CK 0.33%，HA 1.73%) was known as a biocontrol microorganism capable of promoting plant growth.