Initially focused on the European population, multiple genome-wide association studies (GWAS) of complex diseases, such as type-2 diabetes (T2D), Alzheimer disease (AD), have now extended to other populations. However, to date, few ancestry-matched omics datasets have been generated or further integrated with the disease GWAS to nominate the key genes and/or molecular traits underlying the disease risk loci. In this study, we generated and integrated plasma proteomics and metabolomics with the genotype datasets of over 2,300 European (EUR) and 400 African (AFR) ancestries to identify ancestry-specific multi-omics quantitative trait loci (QTLs). In total, we mapped 954 AFR pQTLs, 2,848 EUR pQTLs, 65 AFR mQTLs, and 490 EUR mQTLs.  We further applied these ancestry-stratified QTLs to the risk of metabolic disorders, (e.g. T2D, AD) to pinpoint key proteins and metabolites underlying the disease-associated genetic loci.