Perylene diimide/Carbon nitride (PDI/CN) is an excellent photocatalyst consisting of self-assembled PDI with a π-π stacking structure, and has wide applications. But the effect of PDI morphology over their photocatalytic performance has been scarcely investigated. Herein, we successfully synthesized three different morphologies of PDI, inducement formed by different organic solvents, and coupled them with CN, respectively. For simultaneous production of H2O2 and DFF, their photocatalytic activity has the order of PDI-F/CN > PDI-S/CN > PDI-B/CN. H-stacked PDI-F/CN exhibits good crystallinity, larger specific surface area, higher π-conjugation and large dipole moment, which could improve charge-carrier separation, and its activity was 4.2-fold higher than that of CN. Theoretical calculation results indicated that the PDI-F/CN heterojunction could benefit the adsorption of O2 and 5-HMF and lower the energy barrier, which is an important factor for the enhanced photocatalytic activity. This work provides a new and excellent photocatalyst for biomass oxidation.