The energy of sunlight is predominantly concentrated in near-infrared (NIR) region, posing a paramount limitation for practical application of conventional photocatalysts. Organic semiconductors can offer NIR absorption and tunable energy levels simultaneously through molecular engineering, which presents great potential in solar-driven catalysis. However, an individual organic semiconductor typically generates Frenkel excitons with large binding energy, hindering efficient electron-hole separation. Herein, we develop molecular-level heterojunction to suppress electron-hole recombination, thereby achieving a boosted hydrogen (H2) evolution reaction rate of 25.54 µmol h−1 (12.77 mmol h−1 g−1) under visible–near-infrared (Vis–NIR) light. Surprisingly, heterojunction nanoparticles (NPs) comprising donor polymer PBDB-T matched with an A-D1-D2-D1-A type acceptor BTPT-IC4F exhibit a promising external quantum efficiency of 6.3% at 730 nm. Transient absorption spectroscopy monitors effective extraction of photogenerated holes from the highest occupied molecular orbital (HOMO) of BTPT-IC4F to the HOMO of PBDB-T, while first-principle calculations confirm the prolonged lifetime of excited BTPT-IC4F due to efficient hole capture by the PBDB-T phase. The outstanding performance of heterojunction NPs under NIR light is ascribed to strong hole transfer within the nanoparticle. This study provides valuable insights for designing molecular-level organic heterojunction photocatalysts toward NIR light-driven H2 evolution and other potential reactions.