Single-cell sequencing technologies have become powerful tools for dissecting complex biological processes in aquatic organisms by revealing cellular heterogeneity that is obscured in bulk analyses. This review systematically summarizes recent advances in single-cell RNA sequencing, single-nucleus RNA sequencing, and single-cell multi-omics applied to aquatic research, highlighting methodological developments in cell isolation, microfluidic capture, library construction, and bioinformatic analysis. We further outline representative biological applications of these approaches in studies of skeletal development, immune responses, environmental adaptation, reproductive regulation, and specialized cell types. Despite their considerable promise for aquaculture research, single-cell technologies remain challenged by data sparsity, limited genomic resources for non-model species, and incomplete molecular resolution. Looking ahead, the integration of single-cell multi-omics with spatial transcriptomics and artificial intelligence-driven analytical frameworks is expected to enable the construction of fish-specific cell atlases and accelerate precision breeding, thereby supporting the sustainable development of aquaculture.