Organic thin films composed of highly ordered molecular arrays hold tremendous potential for thermoelectric energy harvesting. In comparison to metal–thiolate arrays formed through covalent bonding, molecular arrays bound to graphene substrates via non-covalent interactions exhibit superior thermoelectric behavior. Recent studies have explored the thermoelectric properties of non-conjugated junctions utilizing graphene as a substrate. However, for energy-harvesting purposes, conjugated oligo-aromatic molecules with narrower HOMO–LUMO gaps are more desirable. The step-wise assembly strategy, which involves using a zinc-centered porphyrin to form a footpad first and subsequently binding the molecular backbones to the regularly arranged zinc centers in the footpad, has been reported as an effective approach for growing conjugated molecular backbone arrays, with minimal intermolecular effects on various types of substrates. In this study, we employ this strategy to fabricate aromatic molecular arrays on graphene substrates. Initially, a zinc-centered porphyrin layer is immobilized onto the graphene substrate through π–π stacking interactions. Subsequently, a conjugated pyridine backbone is coordinated to the zinc tetraphenylporphyrin (ZnTPP). Due to the substantial footprint of ZnTPP, this sequential assembly method effectively separates the molecular backbones and prevents smearing of the density of states arising from intermolecular interactions. Consequently, a significant enhancement in thermopower is achieved. Our findings present a novel approach for designing high-efficiency thermoelectric materials, resulting in a Seebeck coefficient of approximately 51 μV K−1. This value surpasses the majority of reported Seebeck coefficients for organic molecular junctions.