Platycodon grandiflorum is a perennial flowering plant, known as Chinese bell flower, widespread in northeast Asia. The roots of this species are used for centuries to treat diseases, and have extensive pharmacological effects such as reducing adiposity, hyperlipidemia as well as anti-atherosclerotic disorder. In this study, systematical and targeting proteome analysis were executed from the 3, 4 and 5 months aged diploid and tetraploid roots of Platycodon grandiflorum and the proteins were separated by 2-DE and stained by CBB. In diploid roots, a total of 30 protein spots (≥ 2-fold) were analyzed using MASCOT search engine according to the similarity of sequences with previously characterized proteins along with the UniProt database. Among the 30 differentially expressed proteins, 21 proteins sopts were identified as up-regulated and 9 proteins were identified as down-regulated. In contrary, a total of 40 differentially expressed proteins were confirmed from tetraploid roots whereas 28 protein spots were confirmed as up-regulated and 12 proteins were identified as down-regulated. However, the differentially expressed proteins from diploid and tetraploid roots were classified into 12 and 14 possible functional categories respectively using Protein Information Resources. The results revealed that the identified proteins from diploid and tetraploid roots were mainly involved in oxidoreductase activity, nucleotide binding, transferase activity and catalytic activity in bellflower roots. In conclusion, the exclusive proteins from diploid and tetraploid roots may provide insight clues for better understanding the characteristics and functions of proteins and metabolic activity of Platycodon grandiflorum.