Kupffer cells (KCs) are liver‐resident macrophages involved in hepatic inflammatory responses, including nonalcoholic fatty liver disease (NAFLD) development. However, the contribution of KC subsets to liver inflammation remains unclear. Here, using high‐dimensional single‐cell RNA sequencing, we characterized murine embryo‐derived KCs and identified two KC populations with different gene expression profiles: KC‐1 and KC‐2. KC‐1 expressed CD170, exhibiting immunoreactivity and immune‐regulatory abilities, while KC‐2 highly expressed lipid metabolism‐associated genes. In a high‐fat diet–induced NAFLD model, KC‐1 cells differentiated into pro‐inflammatory phenotypes and initiated more frequent communications with invariant natural killer T (iNKT) cells. In KC‐1, interleukin (IL)‐10 expression was unaffected by the high‐fat diet but impaired by iNKT cell ablation and upregulated by iNKT cell adoptive transfer in vivo. Moreover, in a cellular co‐culture system, primary hepatic iNKT cells promoted IL‐10 expression in RAW264.7 and primary KC‐1 cells. CD206 signal blocking in KC‐1 or CD206 knockdown in RAW264.7 cells significantly reduced IL‐10 expression. In conclusion, we identified two embryo‐derived KC subpopulations with distinct transcriptional profiles. The CD206‐mediated crosstalk between iNKT and KC‐1 cells maintains IL‐10 expression in KC‐1 cells, affecting hepatic immune balance. Therefore, KC‐based therapeutic strategies must consider cellular heterogeneity and the local immune microenvironment for enhanced specificity and efficiency.