Using a combined theoretical and experimental approach, a mechanistic understanding of the interactions and pseudocapacitance of different quinone-coupled viologen and pyridiniumium molecules sandwiched between titanium carbide (Ti3C2Tx) MXene layers has been provided. Three different derivatives of quinone-coupled viologen and pyridiniumium are synthesized using nucleophilic substitution reaction and subsequently hybridized with Ti3C2Tx MXene (organic@Ti3C2Tx) using self-assembly approach. The atomic structure of pristine Ti3C2Tx and organic@Ti3C2Tx hybrid films is investigated using grazing incidence X-ray diffraction and X-ray pair distribution function analysis using synchrotron radiation. Spectroscopic results confirm the coupling of quinones with viologen and pyridiniumium molecules and their non-covalent functionalization to the MXene without their catalytic decomposition. First-principles calculations confirm that the preferred orientation of organic molecules upon intercalation/adsorption is horizontal to the Ti3C2Tx surface. The authors reveal that these molecules attach to the Ti3C2Tx surface with a significantly high binding energy (up to −2.77 eV) via a charge transfer mechanism. The electronic structure calculations show that all organic@Ti3C2Tx hybrids preserved their metallic behavior. Free-standing organic@Ti3C2Tx hybrid films show a more than three times higher capacitance at ultra-high scan rates (up to 20 V s−1) compared to their pristine counterpart due to molecular pillaring of organic molecules between Ti3C2Tx layers via strong binding energies and charge transfer.