Calcitonin salmon is an important peptide pharmaceutical, which is mainly used for the treatment of osteoporosis and hypercalcemia. Structurally related peptide impurities in a peptide pharmaceutical probably have side effect or even toxicity, thus needs to be carefully characterized according to pharmacopoeia. With the improvement of analytical techniques, liquid chromatography-high resolution mass spectrometry (LC-HRMS) has become a pivotal technique for the identification and quantification of structurally related peptide impurities in peptide materials. In this study, an LC-HRMS-based method has been developed for the identification and quantification of structurally related peptide impurities in calcitonin salmon material. With this method, 7 peptide impurities (> 1 mg/g) in United States Pharmacopoeia (USP) reference standard and 9 peptide impurities (> 1 mg/g) in European Pharmacopoeia (EP) reference standard were identified and accurately quantified. Besides the peptide impurities reported by USP and EP, several new impurities such as [7-Dehydroalanine] calcitonin salmon, triple-sulfate-calcitonin salmon, [26-Proline] calcitonin salmon, [14-Glutamic acid] calcitonin salmon, [20-Glutamic acid] calcitonin salmon, [26-Aspartic acid] calcitonin salmon, calcitonin salmon acid were observed in the reference standard materials studied. The total mass fractions of all structurally related peptide impurities in calcitonin salmon study materials were estimated to be 57.4 mg/g for USP and 46.3 mg/g for EP with associated expended uncertainties at a 95 % confidence level of 5.2 mg/g (k = 2) and 3.1 mg/g (k = 2), respectively.