Spatial transcriptomics is an important tool for obtaining and analyzing the spatial location information of the transcriptome. In recent years, with the improvement of resolution, throughput and sensitivity, this technology has made significant progress in the field of life sciences. Currently, spatial transcriptomics is widely applied in multiple fields such as biology, medicine and botany. This article reviews the development history of spatial transcriptomics, introduces mainstream technologies, technical selection strategies and related experimental procedures, and summarizes the progress made in the application of spatial transcriptomics in cell type identification and functional analysis, plant growth and development, stress resistance mechanisms and crop breeding. In addition, the article conducts cross-species comparisons from the perspective of spatial transcriptomics, and points out the bottleneck problems existing in the current technological development, such as the balance between resolution and throughput, the particularity of plant tissues, data analysis and standardization. Finally, it looks forward to potential research directions in the future, including technological innovation, assisting molecular biological breeding, and data integration and platform construction, aiming to provide reference and inspiration for related research fields.