Precise spatial and morphological control in the synthesis of semiconductor nanostructures remains a critical challenge for the bottom-up fabrication of integrated nanosystems. Here, we demonstrate that the substrate topography can be used to deterministically control the van der Waals epitaxy of AlN nanostructures on hexagonal boron nitride (h-BN) flakes. Atomic force and scanning electron microscopy studies reveal that vertical AlN nanowires grow randomly on the h-BN surface, while nanowalls preferentially nucleate and propagate along the step edges of h-BN flakes. This morphological selectivity is governed by a critical step height: nucleation of nanowalls occurs only at the steps exceeding a height of 5 ± 1 monolayers of h-BN. In the temperature range from 810 to 850 °C, increasing the growth temperature reduces the nanowire surface density and simultaneously enhances vertical growth of both nanowires and nanowalls. These trends are discussed within a qualitative model. This work establishes a new principle for topographical control over vdW epitaxy, opening a pathway for the fabrication of integrated deep-ultraviolet photonic circuits and ordered piezoelectric nanosystems.