This article presents a facile and generally applicable methodology for the morphology diversification of two-dimensional (2D) nanostructure arrays by modifying angle-resolved heterogeneous shadow mask (AR-HSM). Colloid spheres are used to prepare scalable well-organized monolayer film by self-assembly method and then etched in oxygen plasma to reduce size. Subsequently, the heterogeneous layer is generated by tilted metal deposition technique, then utilized as shadow mask in the substrate etching process, and finally removed by wet etching technique. As a result, the controllable fabrication of a series of complex morphologies, ranging from the crescent structure to the hoof-like structure and the stripes with apexes, is realized. The morphology of the nanostructure array is depend on the profile of the heterogeneous shadow mask (HSM) which is correlated to the incidence angle of the metal vapor. Therefore, a theoretical model is built for the prediction and design of the nanostructure morphology. This AR-HSM aided approach provides a novel and accessible route for the diversification of nanostructure morphology; and can be readily extended to other functional substrates which may be applied in photovoltaic devices or bio-chemical sensors.