Treatments including C （chives monoculture）， F （intercropping chives and pea）， and H （intercropping chives and tomato） were set to analyze the mechanism of intercropping allelopathic crops on the growth and resistance of chives. The effects of intercropping different crops with chives on the composition of endophytic microbial communities in the root system of chives were compared. 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 under the intercropping allelopathic crops. Acidovorax bacteria were the allelopathic combination. There was the dominant endophytic bacterial genus unique to the root system of chives under F （intercropping chives and pea）. Fusarium， Colletotrichum， Plectosphaerella， unclassified_o_Helotiales， and Neocosmospora fungi were the top 5 dominant endophytic fungi genera in the root system of chives under the intercropping allelopathic crops. Gibberella and Acrocalymma fungi were the dominant endophytic fungi unique to the root system of chives under H （intercropping chives and tomato）. Dactylonectria and Myrothecium fungi were the dominant endophytic fungi unique to the root system of chives under F （intercropping chives and pea）. It is indicated that intercropping chives with different crops shaped the composition of endophytic microbial communities in the root system of chives. In the intercropping system of chives， an endogenous microbial community with the functions of promoting crop growth and enhancing crop resistance is formed in the root system of chives. In the intercropping system of chives， an endophytic microbial community dominated by pathogenic microorganisms is formed in the root system of chives， which is one of the important mechanisms for intercropping allelopathic crops with chives as well.