Simultaneous analysis of mRNAs and proteins at the single-cell level provides information about the dynamics and correlations of gene and protein expressions in individual cells, enabling comprehensive study of cellular heterogeneity and expression patterns. Here, we present a platform for about 1000 cellular indexing of mRNAs and membrane proteins, named multi-Paired-seq, with high cell utilization, accurate molecular measurement and low cost. Based on hydrodynamic differential flow resistance, multi-Paired-seq largely improves cell utilization in percentage of cells measured in population (>95%). Combined with pump/valve structure, cell-free antibodies and mRNAs can be removed completely for highly accurate detection (R=0.96) of protein copies. The picoliter reaction chambers allow high detection sensitivity for both mRNA transcripts and protein copies and low sequencing cost. By using multi-Paired-seq, three clusters of known breast cancer cell types are identified according to multimodal measurements, and the expression correlations between mRNAs and proteins under altered conditions are quantified. Multi-Paired-seq provides multi-modal measurements at the single cell level, which offers a new tool for cell biology, developmental biology, drug discovery and precision medicine.