Abstract: 【Objective】 Endophytic fungi have a significant impact on the physiology, development and health of the host, can stimulate the germination and growth of the host plant, and play an important role in regulating the nutrient absorption and enhancing the stress resistance of the host plant. This study aims to reveal the effects of different planting patterns of one-year spring planting (SPS1), two-year spring continuous planting (SPS2) and one-year summer planting (SUS) on the fungal community structure of Isatidis root in Xinjiang. 【Methods】 High throughput sequencing technology was used to identify and analyze endophytic fungi community structure of Radix isatidis root. 【Results】 At the phylum level, endorhizoidal fungi were mainly composed of Ascomycota, Mortierellomycota, Basidiomycota, Chytridiomycota, Olpidiomycota,Blastocladiomycota, Glomeromycota, Rozellomycota and Mucoromycota. Compared with SUS, SPS1 decreased the relative abundance of Neonectria and Penicillium significantly, but increased the relative abundance of Oedocephalum. SPS2 increased the abundences of Ascomycota and Chytridiomycota significantly, but significantly decreased the abundences of Mortierellomycota. However, it increased the relative abundance of Fusarium, Aspergillus, Acremonium, Gibberella and Bisifusarium. Compared with SPS1, SPS2 decreased the relative abundations of Mortierella and Plectosphaerella significantly, but increased the relative abundances of Fusarium, Acremonium and Neonectria. 【Conclusion】 The population structure of endophytic fungi in isatidis root is different under different planting patterns. Continuous planting would decrease the abundance of beneficial fungi and increase the relative abundance of pathogenic fungi and increase the risk of continuous cropping obstacles.