The composite molecular structure model of NH₂-UiO-66/PDINH (UiOxPDy) constructed from NH₂-UiO-66 and PDINH (3,4,9,10-perylenetetracarboxylicdiimide) was built to conduct density functional theory (DFT) calculations for predicting the heterojunction type and corresponding Cr(VI) reduction reaction mechanism. The results of DFT calculations illustrated that Z-scheme heterojunction interface was inclined to form between NH₂-UiO-66 and PDINH via automatically matching the dominant crystal plane, which was in consistent with the results of X-ray photoelectron spectroscopy. Subsequently, the Z-scheme heterojunction UiOxPDy composites (x, y represented the mass of NH₂-UiO-66 and PDINH, respectively) were fabricated via ball-milling treatment, which were used to accomplish effective photocatalytic Cr(VI) reduction under low power LED visible light. The as-prepared optimal UiO125PD75 composite demonstrated good stability and reuse performance in the five runs’ successive operations. The corresponding Cr(VI) reduction mechanism over UiO125PD75 was verified with the aid of electrochemical test, radical scavenging experiments and electron spin resonance.