With an ever?increasing world population and demand for food, ensuring food security has becoming more and more challenging, especially when we are facing severe climate change. However, traditional design breeding is time?consuming and low?efficient, which can’t meet the needs of this era. With the development of sequencing technology, the cost of genotyping and phenotyping continues to decrease, resulting in the explosive growth of omics data. Artificial intelligence, as a tool that can efficiently mine information in big data, has attracted wide attention in the field of biology. Artificial intelligence directed breeding design will greatly accelerate the efficiency of design breeding and bring revolutionary changes. This review introduced the application of artificial intelligence, especially deep learning, in genomics and crop genetic improvement, summarized the application progress, and put forward the prospect of how artificial intelligence design breeding, which was expected to provide new thought for artificial intelligence designed breeding.