With the rapid development of single-cell sequencing technologies, it has become a powerful strategy for the discovery of rare cells and delineating the molecular basis underlying various biological processes. Use of single-cell multimodal sequencing to explore the chromatin accessibility, gene expression and spatial transcriptome has propelled us to success in untangling the unknowns in the enteric nervous system (ENS) and provided unprecedented resources for building new diagnostic framework for enteric neuropathies. Here, we summarize the recent findings of single-cell multimodal sequencing, especially focusing on the most commonly used single-cell RNA sequencing (scRNA-seq) on ENS cells, ranged from the progenitors, neural crest (NC) cells, to the mature ENS circuit, in both human and mouse. These studies have highlighted the heterogeneity of ENS cells at various developmental stages and discovered numerous novel cell types. We will also discuss various computational methods that were used to reconstruct the differentiation trajectories of the developing ENS and to elucidate the cell fate decisions. Profiling disease mechanisms and cellular drug responses with single-cell multimodal omics techniques likely leads to a paradigm shift in the field of biomedical research. Further improvements in the high-resolution sequencing platforms and integrative computational tools will greatly hasten their applications in both the basic and translational medicine.