Comprehensive SummaryPhotocatalytic aerobic oxidative desulfurization (PAODS) is a sustainable alternative technology to traditional, energy‐intensive fuel desulfurization methods. Nonetheless, its advancement is hindered by the notable challenge of inadequate electron‐hole separation efficiency within the existing catalytic systems. Herein, a Janus 2D/2D heterostructure composed of Co3O4 and CoMoO4 is reported for the PAODS of thiophenic sulfides. Through a combination of detailed experimental characterizations and density functional theory (DFT) calculations, we elucidate the formation of a type II p‐n heterojunction in the catalyst, significantly enhancing electron‐hole separation through electric field force and reducing the possibility of electron‐hole recombination due to the spatial separation of redox centres. The photocatalyst exhibits exceptional activity and demonstrates an impressive performance of 10.4 mmol·g–1·h–1 in the oxidation of dibenzothiophene (DBT). Moreover, the photocatalyst demonstrates profound desulfurization capabilities in real diesel, reinforcing its promising prospects for industrial application. These discoveries provide invaluable insights, both scientifically and practically, towards the development of advanced photocatalysts for PAODS processes.