Single-cell RNA sequencing (scRNA-seq) is a revolutionary technology for high-throughput sequencing of RNA within individual cells. Since its introduction in 2009, this technique has undergone continuous updates and iterations, proving to be a transformative tool in the field of life sciences. It has found wide-ranging applications in developmental biology, neurobiology, immunology, microbiology, pharmaceutical research, disease treatment, among other fields, demonstrating broad prospects. The versatility of scRNA-seq lies in its ability to unravel the intricate heterogeneity and complexity of RNA transcripts within cells, thereby facilitating the exploration of different cell types and their functions in organisms. As scRNA-seq technology continues to evolve, with advancements towards multidimensionality and spatial resolution, it has emerged as a powerful tool for dissecting complex biological phenomena at the cellular level. In recent years, the widespread adoption of scRNA-seq has been facilitated by reduced sequencing costs and enhanced technology stability. This has led to its rapid expansion beyond model organisms to non-model species like crops, livestock, and aquatic animals. The extension of scRNA-seq to these organisms has yielded transformative insights into cell heterogeneity and function, marking a paradigm shift in our understanding of these species. Notably, within the realm of aquatic animals, scRNA-seq has gained substantial traction, driving a profound exploration of cellular dynamics and mechanisms underlying various physiological processes. This paper provides a comprehensive overview of scRNA-seq technology, its sequencing methodologies, and its applications in aquaculture animals, alongside a synthesis of relevant research findings. It encapsulates the breadth of scRNA-seq applications in aquaculture, encompassing diverse sample preparation techniques and sequencing platforms while highlighting its inherent advantages in studying aquatic animal biology. Furthermore, it delves into the challenges encountered in applying scRNA-seq to aquatic animals. These challenges include the scarcity of marker genes, limited availability and inconsistent quality of reference genomes, and the need for further experimental refinement in single cell suspension or single nucleus preparation methods. Moreover, this paper offers a forward-looking perspective on potential applications of scRNA-seq in aquaculture, envisaging its role in advancing our understanding of cellular function and regulatory mechanisms in aquatic organisms. By illuminating unexplored avenues for research and innovation, it seeks to inspire further investigations leveraging scRNA-seq to unravel the complexities of cellular dynamics in aquaculture animals. Through interdisciplinary collaboration and technological advancements, scRNA-seq stands poised to catalyze transformative discoveries that will shape the future of aquaculture and contribute to sustainable practices in food production and environmental conservation.