Oxidation and removal of highly toxic sulfides and amines are particularly important for environmental and human security but remain challenging. Here, incorporating an excellent photosensitizer, donor-acceptor-donor (D-A-D)-type 4,4'-(benzo[c][1,2,5]thiadiazole-4,7-diyl)dibenzoic (H2L), into metal-organic frameworks (MOFs) has been manifested to promote the charge separation, affording four three-dimensional (3D) MOFs (isostructural 1-Co/1-Zn with Co2/Zn2 units, and 2-Gd/2-Tb with Gd/Tb-cluster chains) as photocatalysts in the visible light-driven air-O2-mediated catalytic oxidation and removal of hazardous phenylsulfides and benzylamines. Impressively, structure-property correlation illustrated that the transition metal centers assembled in MOFs play an important role in the photocatalytic activity, and we can conclude that 1-Zn can be a robust heterogeneous catalyst possessing good light adsorption and fast charge separation in oxidation removal reactions of both benzylamines and phenylsulfides under visible light irradiation and room temperature with excellent activity/selectivity, stability, and reusability.