IFN-γ-stimulated histocompatibility complex-I (MHC-I) antigen presentation underlies the core of anti-tumor immunity. However, sustained IFN-γ signaling also enhances PD-L1 checkpoint pathway to dampen anti-tumor immunity. It remains unclear how these opposing effects of IFN-γ are regulated. Here we reported that loss of the histone dimethyl transferase WHSC1 impaired the anti-tumor effect of IFN-γ signaling by the transcriptional downregulation of the MHC-I machinery without affecting PD-L1 expression in colorectal cancer (CRC) cells. Whsc1 loss promoted tumorigenesis via a non-cell autonomous mechanism in an Apcmin/+ mouse model, CRC organoids and xenografts. Mechanistically, we identified that IFN-γ-STAT1 signal axis stimulated WHSC1 expression, and in turn WHSC1 directly interacted with NLRC5 to promote MHC-I gene expression, but not PD-L1 level. Concordantly, silencing Whsc1 diminished MHC-I levels, impaired anti-tumor immunity and blunted the effect of immune checkpoint inhibitor (ICB). Patient cohort analysis revealed that WHSC1 expression positively correlated with enhanced MHC-I expression, tumor-infiltrating T cells and favorable disease outcome. Together, our findings establish a tumor-suppressive function of WHSC1 that relays IFN-γ signaling to promote antigen presentation in CRC cells, and provide a rationale for boosting WHSC1 activity in immunotherapy.