Efficient chemical synthesis is critical for the production of organic chemicals, particularly in the pharmaceutical industry. Leveraging machine learning to predict chemical synthesis and improve the development efficiency has become a significant research focus in modern chemistry. Among various machine learning models, the Transformer, a leading model in natural language processing, has revolutionized numerous fields due to its powerful feature-extraction and representation-learning capabilities. Recent applications demonstrated that Transformer models can also significantly enhance the performance in chemical synthesis tasks, particularly in reaction prediction and retrosynthetic planning. This article provides a comprehensive review of the applications and innovations of Transformer models in the qualitative prediction tasks of chemical synthesis, with a focus on technical approaches, performance advantages, and the challenges associated with applying the Transformer architecture to chemical reactions. Furthermore, we discuss the future directions for improving the applications of Transformer models in chemical synthesis.