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Perylene diimide (PDI) derivatives hold great promise as stable, solution‐printable n‐type organic thermoelectric materials, but as of yet lack sufficient electrical conductivity to warrant further development. Hybrid PDI‐inorganic nanomaterials have the potential to leverage these physical advantages while simultaneously achieving higher thermoelectric performance. However, lack of molecular level insight precludes design of high performing PDI‐based hybrid thermoelectrics. Herein, the first explicit crystal structure of these materials is reported, providing previously inaccessible insight into the relationship between their structure and thermoelectric properties. Allowing this molecular level insight to drive novel methodologies, simple solution‐based techniques to prepare PDI hybrid thermoelectric inks with up to 20‐fold enhancement in thermoelectric power factor over the pristine molecule (up to 17.5 µW mK⁻²) is presented. This improved transport is associated with reorganization of organic molecules on the surface of inorganic nanostructures. Additionally, outstanding mechanical flexibility is demonstrated by fabricating solution‐printed thermoelectric modules with innovative folded geometries. This work provides the first direct evidence that packing/organization of organic molecules on inorganic nanosurfaces is the key to effective thermoelectric transport in nanohybrid systems.