Rationale Optimizing the structure of digital polymers is an efficient strategy to ensure their tandem mass spectrometry (MS/MS) readability. In block‐truncated poly(phosphodiester)s, homolysis of C–ON bonds in long chains permits the release of smaller blocks amenable to sequencing. Yet the dissociation behavior of diradical blocks was observed to strongly depend on their charge state. Methods Polymers were ionized in negative mode electrospray and activated in‐source so that blocks released as primary fragments can be investigated using ion mobility spectrometry (IMS) or sequenced in the post‐IMS collision cell. Collision cross sections (CCS) were derived from arrival times using a calibration procedure developed for polyanions using the IMSCal software. A multistep protocol based on quantum methods and classical molecular dynamics was implemented for molecular modeling and calculation of theoretical CCS. Results Unlike their triply charged homologues, dissociation of diradical blocks at the 2– charge state produces additional fragments, with +1 m/z shift for those holding the nitroxide α‐termination and −1 m/z for those containing the carbon‐centered radical ω‐end. These results suggest cyclization of these diradical species, followed by H • transfer on activated reopening of this cycle. This assumption was validated using IMS resolution of the cyclic/linear isomers and supported by molecular modeling. Conclusions Combining IMS with molecular modeling provided new insights into how the charge state of digital blocks influences their dissociation. These results permit to define new guidelines to improve either ionization conditions or the structural design of these digital polymers for best MS/MS readability.