Deciphering epigenetic regulation of gene expression requires measuring the epigenome and transcriptome jointly. Single-cell multi-omics technologies have been developed for concurrent profiling of chromatin accessibility and gene expression. However, multi-omics profiling of low-input bulk samples remains challenging. Therefore, we developed low-input ATAC&mRNA-seq, a simple and robust method for studying the role of chromatin structure in gene regulation in a single experiment with thousands of cells, to maximize insights from limited input material by obtaining ATAC-seq and mRNA-seq data simultaneously from the same cells with data quality comparable to that of conventional mono-omics assays. Integrative data analysis revealed similar strong association between promoter accessibility and gene expression when using the data of low-input ATAC&mRNA-seq as when using single-assay data, underscoring the accuracy and reliability of our dual-omics assay to generate both datum types simultaneously with just thousands of cells. We envision our method to be widely applied in many biological disciplines with limited materials.