Understanding the post-translational modifications of targeted proteins is of great significance for manipulating the physiological processes of eukaryotes. Chemical biology tools have been used to investigate the biological roles of those posttranslational modifications at particular sites, especially genetic code expansion technology, which can also be combined with the concept of synthetic biology to generate a genetically modified organism with a synthetic auxotroph for co-translational modification components. In this concept, we will introduce applications, limitations, and perspectives of genetic code expansion technology for studying post-translational modification based on recent progresses. Future perspectives of genetically modified organisms also will be discussed in regard to the application of post-translational modification research.