Single-cell RNA sequencing (scRNA-seq) is a powerful technology for revealing the heterogeneity of cellular states. However, existing scRNA-seq platforms that utilize bead-based technologies suffer from a large number of empty microreactors and a low cell/bead capture efficiency. Here, Well-paired-seq is presented, which consists of thousands of size exclusion and quasi-static hydrodynamic dual wells to address these limitations. The size-exclusion principle allows one cell and one bead to be trapped in the bottom well (cell-capture-well) and the top well (bead-capture-well), respectively, while the quasi-static hydrodynamic principle ensures that the trapped cells are difficult to escape from cell-capture-wells, achieving cumulative capture of cells and effective buffer exchange. By the integration of quasi-static hydrodynamic and size-exclusion principles, the dual wells ensure single cells/beads pairing with high density, achieving excellent efficiency of cell capture (≈91%), cell/bead pairing (≈82%), and cell-free RNA removal. The high utilization of microreactors and single cells/beads enable to achieve a high throughput (≈105 cells) with low collision rates. The technical performance of Well-paired-seq is demonstrated by collecting transcriptome data from around 200 000 cells across 21 samples, successfully revealing the heterogeneity of single cells and showing the wide applicability of Well-paired-seq for basic and clinical research.