Photocatalysis offers a promising approach for renewable energy conversion and storage, but short lifetimes of charge-separated states in photocatalysts due to charge recombination limit its utility. Here we report an organic molecule with an acceptor–donor–acceptor configuration that can self assemble into highly crystalline nanoparticles. Transient absorption spectroscopy reveals that these crystalline assemblies can induce an ultra-long-lived charge-separated state of up to 1.2 s, attributed to initial symmetry-breaking charge separation, followed by charge hopping across closely packed molecules. These self-assembled nanoparticles have an impressive photocatalytic H₂ evolution rate of 126 mmol g⁻¹ h⁻¹ with an external quantum efficiency of 12% at 550 nm under optimized conditions. This system shows a remarkable stability with 220 million turnover numbers (per particle) over the 77 h of operation. These findings suggest that rational design of organic molecules and their aggregates is vital for improving light-induced charge separation and for developing highly efficient, stable and scalable organic photocatalysts.