Interfacial electron transport in multicomponent systems plays a crucial role in controlling electrical conductivity. Organic–inorganic heterostructures electronic devices where all the entities are covalently bonded to each other can reduce interfacial electrical resistance, thus suitable for low‐power consumption electronic operations. Programmed heterostructures of covalently bonded interfaces between ITO‐ethynylbenzene (EB) and EB‐zinc ferrite (ZF) nanoparticles, a programmed structure showing 67 978‐fold enhancement of electrical current as compared to pristine NPs‐based two terminal devices are created. An electrochemical approach is adopted to prepare nearly π‐conjugated EB oligomer films of thickness ≈26 nm on ITO‐electrode on which ZF NPs are chemically attached. A “flip‐chip” method is employed to combine two EB‐ZnFe2O4 NPs‐ITO to probe electrical conductivity and charge conduction mechanism. The EB‐ZnFe2O4 NPs exhibit strong electronic coupling at ITO‐EB and EB‐NPs with an energy barrier of 0.13 eV between the ITO Fermi level and the LUMO of EB‐ZF NPs for efficient charge transport. Both the DC and AC‐based electrical measurements manifest a low resistance at ITO‐EB and EB‐ZF NPs, revealing enhanced electrical current at ± 1.5 V. The programmed heterostructure devices can meet a strategy to create well‐controlled molecular layers for electronic applications toward miniaturized components that shorten charge carrier distance, and interfacial resistance.