Three isomers of Dy₂O@C₈₈ and two isomers of Dy₂C₂@C₈₈ were synthesized and structurally characterized by single-crystal X-ray diffraction, vibrational spectroscopy, and DFT calculations. Both types of clusterfullerenes feature 4-fold electron transfer to the carbon cage, thus resulting in the same carbon cage isomers identified as C₁(26), C_s(32), and D₂(35). The studies of Dy⋯Dy superexchange interactions in Dy₂O and Dy₂C₂ clusters revealed that the O²⁻ bridge favors antiferromagnetic coupling whereas the acetylide group C₂²⁻ supports ferromagnetic coupling of Dy magnetic moments. The strength of the coupling showed a considerable variability in different cage isomers. All metallofullerenes exhibited slow relaxation of magnetization and magnetic hysteresis. In Dy₂O@C₈₈ isomers the hysteresis remained open up to 7-9 K, while in Dy₂C₂@C₈₈ the hysteresis loops were closed already at 2.5 K. This study demonstrated that both the endohedral bridge between metal atoms and the fullerene cage play an important role in magnetic interactions and relaxation of magnetization.