To provide the background for the genetic engineering modification of cell line, this paper compared two CHO-DG44 cells from different sources in terms of their differences in growth, metabolism and expression of exogenous protein TNFR-FC. ITRAQ combined with 2D LC-MS/MS were used to compare the protein expression profiles between CHO-DG44(A)/TNFR-FC cell, line and CHO-DG44 (B)/TNFR-Fc cell line, and protein-variety, GO enrichment and KEGG enrichment analysis were performed on the differential expression proteins. The results show that there are differences in cell growth, metabolism and exogenous protein expression between the two CHO cells. By comparing the protein expression profiles, it is found that there are 104 up-regulated proteins and 88 down-regulated proteins among 192 differentially expressed proteins. And enzymes accounted for the largest proportion (38.02%) among these differential proteins. The differentially expressed proteins are mainly enriched in biological processes like protein folding, glutathione metabolic process, carbohydrate metabolic process, intracellular protein transport, protein stabilization. These differential proteins are mainly related to pathways such as biosynthesis of amino acids, carbon metabolism, glycolysis/gluconeogenesis, citrate cycle, pyruvate metabolism and other signaling pathways. The differences in growth and metabolism, and expression of exogenous proteins between these two cell lines may be explained by the protomic differences in amino acid biosynthesis, carbon metabolism, glycolysis/gluconeogenesis, etc.