Vertical van der Waals heterostructures (vdWHs), formed through layer-by-layer stacking of two-dimensional materials, offer appealing opportunities for exploring novel physics and potential applications. However, the conventional approach of mechanical exfoliation followed by manual stacking faces significant challenges in achieving atomically clean interfaces and large size, severely limiting practical applications. Here, we proposed a comprehensive mechanism governing nucleation, orientation and stack control of vertical vdWHs during chemical vapour deposition (CVD) and demonstrated the layer-by-layer epitaxial growth of 1 cm × 1 cm sized single-crystal, rhombohedral-stacked WS2/MoS2 films. First-principles calculations reveal that sulphur (S) vacancies in the underlying MoS2 layer preferentially form at step edges. These S vacancies serve as nucleation sites for the upper WS2 layer and enhance symmetry breaking between rhombohedral- and hexagonal-stacked WS2/MoS2. Leveraging this mechanism, we achieved unidirectionally aligned WS2 islands on MoS2 substrate that seamlessly coalesce into continuous single-crystal WS2/MoS2 films. Systematic characterizations confirmed the single-crystal nature and rhombohedral-stacked configuration, while revealing the ferroelectric properties and self-driven photoelectric response in the resulting heterostructures. Our work establishes a fundamental mechanism for controlled growth of single-crystal vertical heterostructures, providing a robust foundation for scalable manufacturing and future industrial applications.