〔Abstract〕 Objective To explore the impact of the status of human epidermal growth factor receptor 2 gene(HER2) gene on the metabolism of gastric cancer with computational gene sets enrichment analysis(GSEA). Methods The expression datasets of gastric cancer were downloaded from the cancer genome atlas(TCGA),gene expression omnibus(GEO) and ArrayExpress. Phenotype labels of Her2 high and low expression were made, which were applied in the GSEA. The meaningful metabolic genesets were found at false discovery rate(FDR) q value<25% and/or nominalPvalue<0.01. Heatmap was made to compare the meaningful gene sets in different datasets. Results Among the 10 datasets including TCGA STAD and GSE66229, peroxisome, N-glycan and pyrimidine metabolisms were significantly affected at FDR q val<25% and nomPval<0.01, glycosylphospatidylinositol GPI anchor biosynthesis, glycerolphosphalipid metabolism and sphingolipid metabolism atPvalue<0.01. Conclusion Multiple metabolic gene sets are affected by Her2 status with evidences in multiple datasets.