Changes in endometrial immune cell density has been reported to be associated with reproductive failure. The prognostic value of endometrial immune cell density measurement remains uncertain. We aimed to investigate the prognostic value of endometrial immune cells measurement on pregnancy outcome after IVF in women. In this prospective study, one hundred twenty-eight women underwent endometrial sampling in a natural cycle preceding single frozen-thawed embryo transfer (ET). Endometrial biopsy was obtained precisely 7 days after luteinizing hormone surge (LH + 7). Multiplex immunohistochemical method was employed to simultaneously stain the endometrium samples with a panel of human antibodies against CD56 for uterine natural killer (uNK) cells, CD3 and CD8 for T cell, CD3 for pan T cells and CD68 for macrophages. The density of the various immune cells and the clustering levels between them were measured. ET was performed at the blastocyst stage. Women who did not conceive had a significantly higher density of uNK cells and higher clustering level between uNK cells-and-macrophages than women who did conceive. In accordance, the prognostic value of uNK measurement on pregnancy outcome was significantly improved when combined with uNK-to-macrophage clustering analysis simultaneously. Taken together, our results suggested that uNK cells density and clustering level between uNK cells-and macrophages may be a promising predictor for successful implantation after IVF-ET.