We introduce a powerful approach based on the combination of size exclusion chromatography with high-resolution mass spectrometry to selectively follow the compaction of discrete polymer chains that have uniform elemental composition. Single-chain nanoparticles (SCNP) have attracted considerable interest for a wide range of applications associated with their adjustable morphology. However, the precise characterization of morphological changes during the compaction is still challenging using existing analysis techniques. We employ a polystyrene backbone functionalized with tetrazole and fumarate moieties to utilize the nitrile imine-mediated tetrazole-ene cycloaddition for compaction. As every compaction step is associated with an elimination of one nitrogen molecule, it can be monitored via high-resolution electrospray ionization mass spectrometry. The combination with size exclusion chromatography enables the direct correlation of changes in mass with changes in morphology associated with the compaction. By establishing a calibration between the retention time and the hydrodynamic radius, ion chromatograms of discrete chains can be directly applied to determine the reduction in hydrodynamic radius associated with each cross-linking event. Therefore, accessing the compaction of discrete polymer chains becomes possible for the first time.