We report an integrated proteogenomic analysis of early onset gastric cancers (EOGCs) using exome and mRNA sequencing and global proteome, phosphoproteome, and glycoproteome profiling. Single amino acid variants (SAAVs) identified by exome sequencing and supported by proteomic and mRNA transcriptomic data enabled effective prioritization of candidate driver genes that are functional at the protein level. Protein abundance changes between paired tumor and adjacent normal tissues were poorly predicted by mRNA transcript abundances, indicating that protein measurements increased the reliable evaluation of cancer-related alterations of cellular processes. Integrated proteogenomic analysis identified four subtypes of EOGCs. Four subtypes were associated with proliferation, immune response, metabolism, and invasion, respectively; and associations of the subtypes with immune- and invasion-related pathways were identified mainly by phosphorylation and N-glycosylation data. Therefore, integrated proteogenomic analysis provided a more complete and better refined molecular characterization of EOGCs than that by genomic analysis alone, affording a paradigm for enhanced understanding of cancer biology and a roadmap for patient stratification as it relates to this disease.