Herein, metal−organic framework (MOF)-based adsorbents are designed with distinct hard and soft metal building units, namely, [Co 2 I Co II (PD) 2 (BP)] (Co_PD-BP) and [Cu 2 ICu II (PD) 2 (BP)] (Cu_PD-BP), where H 2 PD = pyrazine-1,4diide-2,3-dicarboxylic acid and BP = 4,4′-bipyridine. The designed MOFs were characterized via spectral and SCXRD techniques, which confirm the mixed-valent states (+1 and +2) of the metal ions. Topological analysis revealed the rare ths and gwg topologies for Co MOF, while Cu-MOF exhibits a unique 8T21 topology in the 8-c net (point symbol for net: {4 24 •6 4 }). Moreover, severe environmental issues can be resolved by effectively removing heterocyclic organosulfur compounds from fuels via adsorptive desulfurization. Further, the developed MOFs were investigated for sulfur removal via adsorptive desulfurization from a model fuel consisting of dibenzothiophene (DBT), benzothiophene (BT), and thiophene (T) in the liquid phase using n-octane as a solvent. The findings revealed that Cu_PD-BP effectively removes the DBT with a removal efficiency of 86% at 300 ppm and an operating temperature of 25 °C, with a recyclability of up to four cycles. The adsorption kinetic analysis showed that the pseudo-first-order model could fit better with the experimental data indicating the physisorption process. Further, the studies revealed that adsorption capacity increased with the increasing initial DBT concentration with a remarkable capacity of 70.5 mg/g, and the adsorption process was well described by the Langmuir isotherm. The plausible reason behind the enhanced removal efficiency shown by Cu_PD-BP as compared to Co_PD-BP could be the soft−soft interactions between soft sulfur and soft Cu metal centers. Interestingly, density functional theory (DFT) studies were done in order to predict the mechanism of binding of thiophenic compounds with Cu_PD-BP, which further ascertained that along with other interactions, the S•••π and S•••Cu interactions predominate, resulting in a high uptake of DBT as compared to others. In essence, Cu_PD-BP turns out to be a promising adsorbent in the field of fuel desulfurization for the benefit of mankind.