Accurate and reliable quantification of antigen components in vaccines is critical in vaccine quality control and evaluation of immunogenic consistency. However, conventional immunoassays often suffer from limited specificity, trace-level antigen concentrations, and indirect quantification. In this study, we demonstrated an ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method for the determination of effective antigen components in inactivated SARS-CoV-2 vaccines. Specifically, the vaccine samples were denatured and digested with trypsin to generate tryptic peptides. Then, the signature peptides derived from the nucleocapsid protein and their stable isotope-labeled internal standards were selectively captured and separated using anti-peptide antibody-conjugated magnetic beads. The signature peptides were characterized by ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry, which confirmed their amino acid sequence and multi-charged ionization states. Quantitative analysis was then performed using UHPLC-MS/MS in positive electrospray ionization mode with multiple reaction monitoring. Chromatographic separation of the signature peptides was achieved on an ACQUITY Premier Peptide BEH C₁₈ column using 0.1 % formic acid in water and 0.1 % formic acid in acetonitrile as the mobile phases. The method was validated and exhibited excellent linearity for the signature peptides over the concentration range of 1-60 μg/L, with correlation coefficients higher than 0.999. The recovery ranged from 75.1 % to 86.3 %, with intra-day precision (RSD) of 0.8-1.0 % and inter-day precision of 1.3-3.6 %. Finally, the method was successfully applied to determine the effective antigen components in inactivated SARS-CoV-2 vaccine samples. The concentrations of the signature peptide ADETQALPQR ranged from 4.95 to 12.95 µg/L across the three vaccine batches analyzed, corresponding to 4.38-11.47 nmol/L of nucleocapsid protein. The results indicated that the method exhibited great promise for the determination of active antigenic proteins in inactivated SARS-CoV-2 vaccine samples and provided an alternative analytical platform for vaccine quality control.