The increasing application of single-cell RNA sequencing (scRNA-seq) technology in life science and biomedical research has significantly increased our understanding of the cellular heterogeneities in immunology, oncology and developmental biology. This review will summarize the development of various scRNA-seq technologies; primarily discussing the application of scRNA-seq on infectious diseases, and exploring the current development, challenges, and potential applications of scRNA-seq technology in the future. Keywords: 3C, Chromosome Conformation Capture; ACE2, Angiotensin-Converting Enzyme 2; ARDS, acute respiratory distress syndrome; ATAC-seq, Assay for Transposase-Accessible Chromatin using sequencing; BCR, B cell receptor; CEL-seq, Cell Expression by Linear amplification and Sequencing; CLU, clusterin; COVID-19, corona virus disease 2019; CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats; CytoSeq, gene expression cytometry; DENV, dengue virus; FACS, fluorescence-activated cell sorting; GNLY, granulysin; GO analysis, Gene Ontology analysis; HIV, Human Immunodeficiency Virus; IAV, Influenza A virus; IGHV/HD/HJ/HC, Immune globulin heavy V/D/J/C/ region; IGLV/LJ/LC, Immune globulin light V/J/C/ region; ILC, Innate Lymphoid Cell; Infectious diseases; LIGER, Linked Inference of Genomics Experimental Relationships; MAGIC, Markov Affinity-based Graph Imputation of Cells; MARS-seq, Massively parallel single-cell RNA sequencing; MATCHER, Manifold Alignment To CHaracterize Experimental Relationships; MCMV, mouse cytomegalovirus; MERFISH, Multiplexed, Error Robust Fluorescent In Situ Hybridization; MLV, Moloney Murine Leukemia Virus; MOFA, Multi-Omics Factor Analysis; MOI, multiplicity of infection; PBMCs, peripheral blood mononuclear cells; PLAC8, placenta-associated 8; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; SAVER, Single-cell Analysis Via Expression Recovery; SPLit-seq, split pool ligation-based tranome sequencing; STARTRAC, Single T-cell Analysis by RNA sequencing and TCR TRACking; STRT-seq, Single-cell Tagged Reverse Transcription sequencing; Single-cell RNA sequencing; TCR, T cell receptor; TSLP, thymic stromal lymphopoietin; UMAP, Uniform Manifold Approximation and Projection; UMI, Unique Molecular Identifier; mcSCRB-seq, molecular crowding single-cell RNA barcoding and sequencing; pDCs, plasmacytoid dendritic cells; scRNA-seq, single cell RNA sequencing technology; sci-RNA-seq, single-cell combinatorial indexing RNA sequencing; seqFISH, sequential Fluorescent In Situ Hybridization; smart-seq, switching mechanism at 5′ end of the RNA transcript sequencing; t-SNE, t-Distributed stochastic neighbor embedding.