In order to explore the shaping characteristics of chives intercropping and shallot intercropping on the endogenous microbial composition of chives roots, and to explore the effects of different crops on the growth and resistance of chives intercropping, the combination of chives (C), the combined intercropping (H) of chives (Chives/Tomato) and the combined intercropping of Shallot (Chives/Peas) crops (F) were set up to compare and analyze the composition of endogenous microbial communities in the root system of different crops associated with chives. The results showed that unclassified_f__Xanthomonadaceae, Dokdonella, Flavobacterium, unclassified_f__Alcaligenaceae and Devosia were the top 5 dominant endophytic bacterial genera in the root system of chives. At the same time, Acidovorax bacteria are the dominant endophytic bacteria in the root system of chives under the combined intercropping system of chives (chives/peas). Fusarium, Colletotrichum, Plectosphaerella, unclassified_o__Helotiales, and Neocosmospora fungi were the top 5 dominant endophytic fungi genera in the root system of chives intercropping. Gibberella and Acrocalymma fungi are the dominant endophytic fungi in the root system of chives under the combined intercropping system of chives. Dactylonectria and Myrothecium fungi are the dominant endophytic fungi in the root system of chives under the combined intercropping system of chives and peas. The results showed that the intercropping of chives with different crops shaped the composition of endophytic microbial communities with different root systems, and the endophytic microbial communities with the functions of promoting growth and improving resistance were formed in the roots of chives in the chives intercropping system. In the chives intercropping system, an endophytic microbial community with pathogenic microorganisms as the main body was assembled in the root system of chives, which was also one of the important mechanisms for the intercropping of chives to produce the phenomenon of mutual restraint in different crops.