Intestinal organoid is a new experimental model and is widely used in research on intestinal diseases and functional changes for its property in mimicking structures and functions of in vivo organs. In recent years，researchers have combined gene-editing technology with intestinal organoids，offering possibilities for elucidating the mechanisms of diseases and developing targeted therapies for these diseases. This review looks back on the applications of gene-editing in intestinal organoids and their future perspectives in disease modeling and drug development.