The population genomics boom has opened up a new era for precision medicine. Vietnam, the world’s 16th most populous country, with a long migratory history, remains underrepresented in all global genomic databases. Here, we present VN1K, the first comprehensive and deeply-curated resource of multi-omics data with a wide-range of phenotypic information including demographic, anthropometric, biochemical, and clinical traits of 1,011 unrelated Vietnamese individuals from 54 provinces and cities across all three main regions of Northern, Central, and Southern Vietnam. First, whole-genome sequencing (WGS), high-depth short-read data were generated for all samples, then microarray data were produced for selected samples. In addition, WGS long-read data were generated for selected samples using both PacBio and Oxford Nanopore long read sequencing platforms, generating the first whole-genome methylation profile for Vietnamese. Finally, RNA-Seq data of selected samples were generated for gene expression and regulation analysis. Our ultra-sensitive variant detection pipeline, utilizing a custom-built pangenome graph reference combined with a deep-learning framework, identified 40 million variants, of which 8.5 million were novel (incl. 896 thousand short insertions/deletions and 39 thousand structural variants). As a result, VN1K provides the highest accuracy imputation panel of the Vietnamese population, especially on highly polymorphic regions such as human leukocyte antigens and pharmacogenes. Variants with significantly different allele frequencies in the Vietnamese population compared to others were found to be functionally significant, especially in genes associated with genetic disorders (incl. GCNT2, PMFBP1, HNRNPUL2, BSCL2), immune diseases (incl. HLA-B, KIR3DL3, and KIR2DL1), and drug responses (incl. CYP2C19, CYP2D6, VKORC1, CYP2B6). All data and results can be accessed via MASH (genome.vinbigdata.org), a large-scale genomic data portal with an integrated linear- and graph-based genome browser to facilitate data analysis and visualization. In summary, VN1K elucidates the landscape of Vietnamese functional genotypes, providing a springboard for precision genomics and epigenomics for Vietnam.