A novel g-C3N4/PDI@MOF heterojunction was synthesized by the in situ growth of NH2-MIL-53(Fe) onto the g-C3N4/PDI layer. The heterojunction was applied as a photocatalyst for the removal of pharmaceutical and phenolic micropollutants in the present of H2O2 and visible LED light (420 < lambda < 800nm). The synergistic heterojunction displays excellent photocatalytic performance for the removal of several water-soluble and toxic organic pollutants (50 ppm) under visible light irradiation, with a maximum efficiency of up to 90% (1 h) for tetracycline (TC), 78% (2.5 h) for carbamazepine (CBZ), 100% (10 min) for bisphenol A (BPA) and 100% (30 min) for p-nitrophenol (PNP). Furthermore, the low concentration of phenolic organic pollutants (2 ppm) can also be rapidly degraded into small molecules (analyzed by HPLC) within 10 min. This performance is superior to some previously reported visible-light photocatalysts. The improved photocatalytic activity is attributed to the efficient formation of heterojunctions derived from the interface contact and electronic band structure matching between g-C3N4/PDI and NH2-MIL-53(Fe), which is beneficial to charge separation and facilitates the photodegradation process. Repeated experimental studies and structural analysis of photocatalyst before and after degradation (XRD and FT-IR) demonstrated that the photocatalyst exhibits good stability and reusability. This work provides a new insight into the construction of heterojunction photocatalysts based on FeMOF for the heterogeneous photodegradation of organic contaminants with H2O2 under visible light.