The application of two-dimensional (2D) graphitic carbon-based materials in photocatalysis has been limited to date, because the nature and role of π-conjugated moieties in them remain unclear. Herein we propose and study bilayer BC₃/C₃N and BC₃/BC₆N van der Waals heterostructures as direct Z-scheme photocatalysts for overall water splitting using density functional theory calculations. The roles of polar π-conjugated moieties in the formation, stacking configuration, and electronic and optical properties of bilayer van der Waals heterostructures are discussed. It is shown that polar π-conjugated moieties of graphitic BCN monolayers lead to a favorable π–π interaction, determining the most stable stacking configuration, and a long-range charge transfer between components. The former makes the electronic band structure of heterostructures favor photocatalytic water splitting in efficiency and energetics. The latter generates a built-in electric field for the interface recombination of photogenerated electron–hole pairs, indicating a Z-scheme mechanism. The delocalized nature of π-conjugated electrons in monolayer components allows for high carrier mobility of bilayer heterostructures, promoting the photocatalytic reactions on graphitic BCN monolayers. These findings show that 2D π-conjugated materials, including graphitic carbon-based materials and biological systems, have great potential in the design and development of 2D metal-free direct Z-scheme photocatalysts for environmental purification and energy conversion.