According to the requirements of the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH), the structures of impurities in pharmaceutical products present at over 0.1% need to be confirmed. Therefore, the aim of this study is to separate and identify the impurities in cephapirin sodium drug substances, so as to guide the industry to improve the production process and storage conditions and reduce the amount of impurities in the product. In the first chromatography dimension, a Boston Green ODS (4.6 mm × 250 mm, 5 μm) column was used, with a mobile phase composed of 0.05 M sodium dihydrogen phosphate aqueous solution and acetonitrile. In the second dimension, the column was a Shimadzu Shim-pack GISS C18 (50 mm × 2.1 mm, 1.9 μm), using 10 mM ammonium formate solution and methanol as the mobile phase. The fragmentation behavior of cephapirin and its impurities and isomers was studied and the structures of impurities were deduced based on the MSn data. For six unknown impurities tentative structures were proposed. The degradation behavior of cephapirin sodium was also studied. Impurities 1 to 11 were found in commercial cephapirin sodium samples, indicating that cephapirin sodium should be stored in closed containers. The contradiction between the non-volatile mobile phase and mass spectrometry was solved by means of multiple heart-cutting approaches and an on-line desalting technique. Twelve impurities and isomers were separated and characterized. These results could be used to improve the methods described in pharmacopoeias for the quality control of cephapirin sodium.