Hemophagocytic lymphohistiocytosis (HLH) is a potentially fatal systemic inflammation disease in children. The most common cause is Epstein-Barr virus (EBV) infection. MHC class I polypeptide-related sequence B (MICB) is a membrane protein inducibly expressed upon cellular stress, viral infection, or malignant transformation, thus marking these cells for clearance through natural killer group 2 member D-positive lymphocytes. MICB can be released into plasma through several mechanisms, reducing NK cell cytotoxicity. We conducted clinical research on HLH patients and cell research in vitro. In the retrospective clinical part, 112 HLH patients (including EBV-HLH group and non-EBV-HLH group), 7 infectious mononucleosis patients, and 7 chronic active EBV infection patients were treated in Beijing Children's Hospital, affiliated with Capital Medical University, from January 2014 to December 2020, were enrolled in this study. Real-time quantitative polymerase chain reaction, standard enzyme-linked immunosorbent assay methods, and lactate dehydrogenase release tests were used to examine the expression of MICB mRNA, the soluble MICB (sMICB) levels, and the activity of NK cells in those patients. In vitro research, MICB overexpression-vector virus, MICB knockdown-vector virus, and empty-vector virus were transfected into two kinds of target cells, such as K562 and MCF7. The level of sMICB and NK cell killing activity between other groups was compared. Finally, we compared NK92 cell killing activity in different concentrations of sMICB. In clinical studies, compared with the non-EBV-HLH group, the EBV-HLH group had lower NK cell killing activity ( P < 0.05). The level of sMICB in the EBV-HLH group was significantly higher than in non-EBV-HLH, infectious mononucleosis, and chronic active EBV infection patients ( P <0.05). A high level of sMICB was associated with poor treatment response and poor prognosis ( P <0. 05). Cellular studies showed that an increased level of membrane MICB could positively correlate with the killing activity of NK92 cells ( P <0. 05), and a high level of sMICB (1250 to 5000pg/ml) could reduce the killing activity of NK92 cells ( P < 0.05). A high level of sMICB (2500pg/ml) could increase the release of cytokines from NK92 cells. The expression level of sMICB in EBV-HLH patients increased, and a high level of sMICB at the initial onset indicated a poor treatment response. The killing activity of NK cells in EBV-HLH patients decreased more significantly. The high level of sMICB may inhibit the killing activity but increase the release of cytokines of NK92 cells.