The Million Microwell Device (MMD) is a high-throughput and low-cost platform for single-cell isolation and RNA sequencing. The MMD is made of biocompatible PDMS material and contains 1,000,000 high-quality cylindrical microwells of 30 µm in diameter and 33 µm in depth. The optimized size of microwells is compatible with efficient single-cell isolation of most cells. The MMD allows to easily generating up to 100,000 pairings of single cells and single barcoded magnetic beads into single microwells. The single cell-bead pairings can be clearly identified through bight field, phase contrast, and fluorescence imaging under a x10, x20, and x40 objective. In microwells, the isolated single cells are lysed and their mRNA are captured by the paired barcoded mRNA capture beads for subsequent transcriptome sequencing.