Photocatalysts based on organic heterojunction nanoparticles (NPs) have recently attracted a rising interest for photocatalytic hydrogen (H2) evolution (PHE), which demands an in-depth understanding of the correlation between their molecular structure and PHE properties. In this work, three n-type, small-molecule electron acceptors, namely ITIC, IT-4F, and IDMIC, with varied end groups and alkyl chain lengths are utilized to prepare organic heterojunction NP photocatalysts with the p-type electron donor PM6, and their PHE properties and operational stabilities are characterized and correlated with their structural differences. Our results show that the PM6:ITIC heterojunction NPs only enable a low H2 evolution reaction (HER) rate, which is enhanced in the PM6:IT-4F system due to its improved light absorption and more efficient exciton separation capabilities after molecular fluorination. Encouragingly, because of the reduced alkyl chain lengths, the PM6:IDMIC heterojunction NPs exhibit a more efficient exciton separation and a superior Pt loading ability, which translates to HER rates of 328 and 22 mmol g–1 h–1 with Pt additions of 15 and 2 wt %, respectively, which are among the highest values for photocatalysts. Moreover, the PM6:IDMIC heterojunction NPs also demonstrate the best operational stability due to having the slowest NP aggregation and photochemical degradation.