The construction of heterojunctions is widely accepted to promote charge separation and transfer efficiency, aimed at improving photocatalytic performance. Herein, NH2-UiO-66 (Zr)/PDI (NUPDI) n-n heterojunction photocatalysts were successfully synthesized via a facile self-assembly method. The formed NUPDI heterojunction photocatalysts exhibited high photocatalytic performance and stability for Cr (VI) reduction, and the corresponding removal rate reached 99.5% at the optimized NUPDI (1:8) under visible light irradiation for 120 min. The introduction of SA-PDI not only enhances the visible light response range of NH2-UiO-66 (Zr), but also generates more photo-generated carriers. Simultaneously, the formation of π-π interaction between NH2-UiO-66 (Zr) and SA-PDI greatly facilitates the charge separation. Furthermore, the possible Z-scheme mechanism is illustrated and analyzed between NH2-UiO-66 (Zr) and SA-PDI, which effectively inhibits the recombination of photo-generated electrons and holes, thereby enhancing the capability of photocatalytic reduction. Overall, this work would provide a potential approach for constructing heterojunction photocatalysts of supramolecular organic materials and metal-organic framework materials for wastewater purification.