Development of nano‐structured metal oxides/heteroatom composites with controlled components and structure for photochemical oxidation still remains a great challenge. Here, a new and versatile strategy is reported for transformation of organonitrogen‐encapsulated metal‐organic frameworks (MOFs) into N‐doped Fe3O4@C nanopolyhedron by chemical vapor deposition‐induced super‐assembly method. Strong confined interaction between organonitrogen guests (urea, thiourea, melamine, and dimethylimidazole) and Fe nodes of MOFs realizes reconstruction of crystal structure and introduction of N species. With the novel approach, the uniform dispersion of guests and perfect metallic/heteroatom interfacial is obtained. Compared with MOFs‐derived Fe2O3/C, the heteroatom/defect‐to‐metal cluster charge transfer excitations lead N‐doped Fe3O4@C to exhibit more superior activity for photocatalytic oxidation (turn‐over frequencies as high as 3.72 h−1). It demonstrates that the introduction of abundant pyrrole‐N and oxygen vacancies on carbon interface boosts the advance of photo‐generated carrier transfer. The study offers a simple and promising strategy for the design of novel metal oxides/heteroatom composite with adjustable structure and functions.