Organoid is a multicellular cluster formed by tissue stem cells cultured in 3D in vitro, which has the ability of self-proliferation and multi-directional differentiation. Due to it is similar to the gene, structure and function of the source organ in space and structure, it can be used to simulate the growth, differentiation and organ formation process of tissue cells in vivo, drug screening and evaluation, biomedical materials and tissue engineering. Increasing evidence shows that different kinds of organs and tissues can be used to simulate the process of pathogen invasion in vitro. This review summarizes the research progress and application prospect of organoids model in pathogenic infection related diseases.