In current top‐down nanofabrication methodologies the design freedom is generally constrained to the two lateral dimensions, and is only limited by the resolution of the employed nanolithographic technique. However, nanostructure height, which relies on certain mask‐dependent material deposition or etching techniques, is usually uniform, and on‐chip variation of this parameter is difficult and generally limited to very simple patterns. Herein, a novel nanofabrication methodology is presented, which enables the generation of high aspect‐ratio nanostructure arrays with height gradients in arbitrary directions by a single and fast etching process. Based on metal‐assisted chemical etching using a catalytic gold layer perforated with nanoholes, it is demonstrated how nanostructure arrays with directional height gradients can be accurately tailored by: (i) the control of the mass transport through the nanohole array, (ii) the mechanical properties of the perforated metal layer, and (iii) the conductive coupling to the surrounding gold film to accelerate the local electrochemical etching process. The proposed technique, enabling 20‐fold on‐chip variation of nanostructure height in a spatial range of a few micrometers, offers a new tool for the creation of novel types of nano‐assemblies and metamaterials with interesting technological applications in fields such as nanophotonics, nanophononics, microfluidics or biomechanics.