Agricultural genomics has developed rapidly with a significant increase in information and data. This article summarized the development process of global agricultural genomics in recent years from the perspective of research topic intensity, change paths and research progress. The search strategy used agricultural genome keywords, which were searched from January 2001 to December 2021. Finally, the SCI and SSCI paper datasets were constructed in the Web of Science database, and the topic intensity index system was used to measure the attention and research heat of each cluster. In recent years, the global agricultural genome had achieved remarkable results, transitioning from fundamental exploration to targeted breakthroughs in agricultural applications, and the similarity of research directions increased gradually. In the future, global research hotspots in agricultural genomics would shift towards more multidimensional and high-precision research such as correlation, diversity, and accuracy. Breakthroughs in complete genome, complex genome, and pan genome research and technology, as well as the development of gene chips, those still faced challenges. The results of this article had significant implications for achieving data-based scientific decision-making and technological innovation.