Advances in single-cell long-read sequencing technologies have significantly enhanced the ability to study cellular heterogeneity and complex biological processes at the single-cell level. Long-read sequencing allows for the accurate identification of RNA isoforms, structural variants, and epigenetic modifications, providing deeper insights into cellular complexity and potential applications in drug development. Single-cell long-read RNA sequencing (scRiso-seq) enables high-quality transcript assembly, structural variant detection, and the characterization of epigenetic modifications. This review discusses the advancements in scRiso-seq, the challenges in downstream analysis, and complementary technologies for single-cell genome, epigenome, and epitranscriptome sequencing. It highlights the integration of long-read sequencing into existing scRNA-seq pipelines and the challenges in library preparation, sequencing, and data analysis. The review also discusses the choice of long-read sequencing platforms, the analysis of scRiso-seq data, and the identification and correction of cell barcodes and unique molecular identifiers (UMIs). The review emphasizes the importance of accurate isoform-level quantification and the challenges in detecting rare isoforms and cell populations. It also addresses the need for improved bioinformatics tools and pipelines for scRiso-seq, as well as the challenges in single-cell long-read sequencing of the genome, epigenome, and epitranscriptome. The review concludes with a discussion of the future directions for single-cell long-read sequencing technologies, including the development of new library preparation protocols and data analysis pipelines to address current limitations and expand the applications of these technologies in biomedical research.Advances in single-cell long-read sequencing technologies have significantly enhanced the ability to study cellular heterogeneity and complex biological processes at the single-cell level. Long-read sequencing allows for the accurate identification of RNA isoforms, structural variants, and epigenetic modifications, providing deeper insights into cellular complexity and potential applications in drug development. Single-cell long-read RNA sequencing (scRiso-seq) enables high-quality transcript assembly, structural variant detection, and the characterization of epigenetic modifications. This review discusses the advancements in scRiso-seq, the challenges in downstream analysis, and complementary technologies for single-cell genome, epigenome, and epitranscriptome sequencing. It highlights the integration of long-read sequencing into existing scRNA-seq pipelines and the challenges in library preparation, sequencing, and data analysis. The review also discusses the choice of long-read sequencing platforms, the analysis of scRiso-seq data, and the identification and correction of cell barcodes and unique molecular identifiers (UMIs). The review emphasizes the importance of accurate isoform-level quantification and the challenges in detecting rare isoforms and cell populations. It also addresses the need for improved bioinformatics tools and pipelines for scRiso-seq, as well as the challenges in single-cell long-read sequencing of the genome, epigenome, and epitranscriptome. The review concludes with a discussion of the future directions for single-cell long-read sequencing technologies, including the development of new library preparation protocols and data analysis pipelines to address current limitations and expand the applications of these technologies in biomedical research.