Human C-peptide is secreted in equimolar amounts with insulin by pancreatic beta-cells. Measurement of C-peptide plays an important role in the diagnosis and treatment of diabetes where it is used to evaluate the function of islet cells. However, C-peptide measurement results across different laboratories vary considerably and there is an urgent need to improve comparability between laboratories. As it is sensitive and specific, isotope dilution-liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS) has made a major contribution and will continue to play a significant role in the standardization of C-peptide measurement. Here, we reviewed the application of ID-LC-MS/MS in C-peptide measurement by discussing the biochemical properties of C-peptide, common sample preparation procedures, and the sensitivity problems often encountered with ID-LC-MS/MS C-peptide measurement. Collectively, these factors are crucial for the development of ID-LC-MS/MS methods for C-peptide measurement. We also discussed the advantages, disadvantages, and progress of implementing ID-LC-MS/MS as a routine measurement tool for C-peptide in clinical laboratories. Finally, we summarized the existing reference system and the status of C-peptide measurement in clinical laboratories to convey the necessity of improving the comparability of C-peptide measurement in clinical laboratories using ID-LC-MS/MS.