The offspring generated by assisted reproductive technology (ART) are considered genetically identical with those generated by natural fertilization. However, studies have found that there are differences between them in some phenotypes to varying extents. In this review, we have summarized the effects of ART on the sex ratio, growth and development, behavior, life expectancy, metabolism of organs and tissues, and molecular phenotypes of mice, providing some guidance to the problems that may arise during the application of ART in the production of genetically modified mice, rapid propagation, purification, embryo cryopreservation, and so on.