The existence of Lactobacillus-led colonized bacteria in the endometrium of a healthy human has been reported in recent studies. Unlike the composition of the microbiome in the lower genital tract, that in the endometrium is different and closely associated with the physiological and pathological processes of gynecological diseases. For example, changing the immune microenvironment affects the receptivity of the endometrium, thereby leading to abnormal reproductive outcomes, such as embryo implantation failure and recurrent spontaneous abortion. However, the concrete functions and mechanisms of the endometrial microbiome have not been studied thoroughly. This review elaborates the research progress on the mechanisms by which the endometrial microbiome affects endometrial receptivity from the perspective of endometrial immune microenvironment regulation. Considering the lack of a unified evaluation method for the endometrial microbiome, as well as the lack of an optimal treatment protocol against recurrent spontaneous abortion, we also discussed the application of combining antibiotics with probiotics/prebiotics as precautionary measures.