AbstractRobust allogeneic immune reactions after transplantation impede the translational pace of human embryonic stem cells (hESCs)‐based therapies. Selective genetic editing of human leucocyte antigen (HLA) molecules has been proposed to generate hESCs with immunocompatibility, which, however, has not been specifically designed for the Chinese population yet. Herein, we explored the possibility of customizing immunocompatible hESCs based on Chinese HLA typing characteristics. We generated an immunocompatible hESC line by disruptingHLA‐B,HLA‐C, andCIITAgenes while retaining HLA‐A*11:01 (HLA‐A*11:01‐retained, HLA‐A11R), which covers ~21% of the Chinese population. The immunocompatibility of HLA‐A11RhESCs was verified by in vitro co‐culture and confirmed in humanized mice with established human immunity. Moreover, we precisely knocked an inducible caspase‐9 suicide cassette into HLA‐A11RhESCs (iC9‐HLA‐A11R) to promote safety. Compared with wide‐type hESCs, HLA‐A11RhESC‐derived endothelial cells elicited much weaker immune responses to human HLA‐A11+T cells, while maintaining HLA‐I molecule‐mediated inhibitory signals to natural killer (NK) cells. Additionally, iC9‐HLA‐A11RhESCs could be induced to undergo apoptosis efficiently by AP1903. Both cell lines displayed genomic integrity and low risks of off‐target effects. In conclusion, we customized a pilot immunocompatible hESC cell line based on Chinese HLA typing characteristics with safety insurance. This approach provides a basis for establishment of a universal HLA‐ARbank of hESCs covering broad populations worldwide and may speed up the clinical application of hESC‐based therapies.