Halogenated nucleosides are known candidates for enhancing X-ray damage in radiotherapy of tumors and are also excellent model systems for investigating molecular and charge dynamics following deep inner-shell ionization. We carried out electron–multi-ion coincidence measurements with two gas-phase halogenated deoxyuridine derivatives – 5-iodo-4-thio-2′-deoxyuridine (ISDU) and 5-bromo-4-thio-2′-deoxyuridine (BrSDU). We report the fragmentation patterns and kinetic energies of ions in coincidence with the I 2p, Br 2p and S 1s photoelectrons, complementing the experiment with molecular mechanics simulations and developing the parametric, stochastic model further. This work demonstrates the applicability of the multiparticle energy- and momentum-resolved coincidence technique to the relatively unexplored regime of incomplete Coulomb explosion of a biomolecular system charged up by deep inner-shell Auger cascades. Simulations of the incomplete Coulomb explosions are carried out to compare with, and complement the experimental data. Their good overall agreement shows the expected trend of more energetic Coulomb explosions and an increased degree of atomization as deeper atomic inner-shells are ionized. The presented data on ion abundances and kinetic energies extend beyond these general predictions, providing essential input for modeling the subsequent damage propagation into the surrounding environment – an aspect directly related to the radiosensitizing properties. Some observables, such as the kinetic energies of halogen ions, are particularly sensitive to the interplay of the charge and nuclear dynamics and provide valuable benchmarks for model development.