Graphdiyne (GDY) is an ordered two-dimensional (2D) carbon allotrope comprising sp- and sp2-hybridized carbon atoms with high degrees of π-conjugation, which features a natural band gap and superior electric properties. However, the synthesis of one- or few-layer GDY remains challenging because of the free rotation around alkyne-aryl single bonds and the lack of thickness control. We report the facile synthesis of an ultrathin single-crystalline GDY film on graphene through a solution-phase van der Waals epitaxial strategy. The weak admolecule-substrate interaction at the heterojunction drastically relaxes the large lattice mismatch between GDY and graphene. It allows the fast in-plane coupling of admolecules and slow out-of-plane growth toward the formation of an incommensurately stacked heterostructure, which is composed of single-layer graphene and few-layer ABC-stacked GDY, as directly observed by electron microscopy and identified from Raman fingerprints. This study provides a general route not only to the bottom-up synthesis of intriguing 2D acetylenic carbon allotropes but also to the device fabrication for the direct measurement of their intrinsic electrical, mechanical, and thermal properties.