Single‐cell RNA sequencing (scRNA-seq) has emerged as a transformative technology in the field of biological science, providing a powerful tool for elucidating cell heterogeneity, tracing cell lineage, and understanding immune response mechanisms, among other applications. In recent years, scRNA-seq has found widespread application in aquaculture animals. This paper presents a comprehensive review of the development, principles and application of scRNA-seq technology in the context of aquaculture animals. Additionally, we analyze existing challenges and project future development trends to promote the application of scRNA-seq in aquaculture, thereby accelerating research in the regulation mechanisms of life activities at the single-cell level in aquatic animals.