Supramolecular isomerism has been recognized as an effective strategy for manipulating structures and properties, particularly in metal−hydrogen-bonded organic frameworks (MHOFs). However, it has been less studied in the context of magnetic dynamics. In this study, we reinvestigated two previously reported cobalt(II) HOFs, {[(), which exhibit unique supramolecular isomerism. In both complexes, octahedral Co(II) ions are connected by deprotonated Hbic-ligands to form one-dimensional chains, which are then sustained into three-dimensional frameworks by prominent N−H•••O hydrogen-bonding interactions. This results in significantly different porosities and N 2 -adsorption abilities: a high solvent-accessible void of 46.2% for the desolvated phase of 1, compared to only 2.3% for that of 2, likely due to the additional π−π stacking interactions. Interestingly, our magnetic studies revealed that both 1 and 2 exhibit typical single ion magnet behaviors, with alternating relaxation dynamics (Raman, direct, and QTM for 1; Raman and direct for 2). These findings demonstrate that the structures, stability, porosities, and magnetic properties of MHOF materials can be effectively tuned through a supramolecular isomerization approach.