Nanofabrication is continuously searching for new methodologies to fabricate 3D nanostructures with 3D control over their chemical composition. A new approach for heterostructure nanorod array fabrication through spatially controlled–growth of multiple metal oxides within block copolymer (BCP) templates is presented. Selective growth of metal oxides within the cylindrical polymer domains of polystyrene‐block‐poly methyl methacrylate is performed using sequential infiltration synthesis (SIS). Tuning the diffusion of trimethyl aluminum and diethyl zinc organometallic precursors in the BCP film directs the growth of AlOx and ZnO to different locations within the cylindrical BCP domains, in a single SIS process. BCP removal yields an AlOx‐ZnO heterostructure nanorods array, as corroborated by 3D characterization with scanning transmission electron microscopy (STEM) tomography and a combination of STEM and energy‐dispersive X‐ray spectroscopy tomography. The strategy presented here will open up new routes for complex 3D nanostructure fabrication. A new approach for the design and fabrication of 3D metal oxide heterostructure nanorod arrays is realized through spatially controlled–growth of multiple metal oxides within self‐assembled block copolymer films. Tuning the metal oxide precursor diffusion enables control over the 3D nanorod chemical composition in a simple and precise process.