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 Fe 3 O 4 @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 Fe 2 O 3 /C, the heteroatom/defect-to-metal cluster charge transfer excitations lead N-doped Fe 3 O 4 @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.