Protoporphyrinogen oxidase (PPO, EC 1.3.3.4), as a key enzyme in chlorophyll biosynthesis, plays an important role in the development of novel herbicides. In this study, the 3-(pyridin-2-yl)benzothiazol-2-one scaffolds were integrated with uracil-based pharmacophores through hybridization strategies to develop innovative molecules with the dual advantages of enhancing herbicidal activity and improving crop safety. Starting from substituted anilines, a total of 25 benzothiazol-2(3H)-one derivatives were synthesized via a multistep synthetic protocol, and their structures were characterized by 1H and 13C NMR and single-crystal X-ray diffraction analysis (for B-04). Pot experiments revealed that B-04 exhibits excellent post-emergence herbicidal activity against broadleaf weeds. Notably, it demonstrates potent pre-emergence activity against both dicotyledonous and monocotyledonous weeds, showing efficacy comparable to that of flumioxazin. Furthermore, B-04 exhibited favorable crop safety as a selective pre-emergence herbicide in soybean, peanut, and cotton cultivation systems. This study developed a novel N-phenyl heterocyclic herbicide featuring a 3-(pyridin-2-yl)benzothiazol-2-one scaffold.