Cellular heterogeneity is essential to biological processes, such as embryonic development, cell differentiation, and the progression of disease. Recent years have seen the development of a variety of single-cell multi-omics technologies that systemically co-detect the genome, epigenome, transcriptome, and proteome for single-cell heterogeneity evaluation comprehensively. Microfluidics has emerged as a significant tool for single-cell multi-omics techniques, enabling the analysis of the complex regulatory network associated with genome coding, epigenome regulation, and transcriptome/proteome expression in a single cell with increased detection sensitivity, accuracy, throughput, and integration. A review of state-of-the-art microfluidic single-cell multi-omics analysis is presented here. Various microfluidics for isolating single cells are introduced first, highlighting their advantages, disadvantages, and applications in single-cell sequencing. Then a comprehensive overview of microfluidic single-cell multi-omics techniques is provided. In addition, a brief introduction of single-cell multi-omics analysis in biological applications and clinical settings will be presented. Finally, we will conclude by discussing the future challenges and prospects of this field.