Natural Killer (NK) cells are effector lymphocytes involved in tumor immunosurveillance, however, the specific mechanism in hepatocellular carcinoma (HCC) has not been well understood. In the present study, we estimated the relative abundances of NK cells in HCC using gene expression data, and found that NK cell abundance was lower in HCC tissues than in the adjacent normal tissues. With the common HCC subclasses, we also found that three HCC subclasses had distinct abundances of NK cells. Moreover, we also found strong association between NK cell abundances and genes encoding immune checkpoint proteins, such as KLRD1, CD96, TIGIT, CD86, HAVCR2, PDCD1 (PD-1), HLA-E, CD274 (PD-L1), and CTLA4, among which, KLRD1 vs. HLA-E, CD274 vs. PDCD1, and CTLA4 vs. CD86 were three pairs of receptors and ligands. Furthermore, we investigated the clinical significance of NK cell activities in HCC, and found that the NK cell abundances were highly associated with the response to sorafinib, and higher NK cell abundances may prolong both the recurrence-free and overall survival of HCC patients. In summary, the present study not only improved our understanding of the potential tumor immune evasion mechanism of NK cells in HCC, but also proposed the potential clinical application of NK activities in HCC treatment and risk assessment.