Protoporphyrinogen oxidase (PPO, EC 1.3.3.4) is an effective target for green herbicide discovery. In this work, we reported the unexpected discovery of a novel series of -phenylaminomethylthioacetylpyrimidine-2,4-diones (-) as promising PPO inhibitors based on investigating the reaction intermediates of our initially designed -phenyluracil thiazolidinone (). An efficient one-pot procedure that gave 41 target compounds in good to high yields was developed. Systematic PPO (NtPPO) inhibitory and herbicidal activity evaluations led to identifying some compounds with improved NtPPO inhibition potency than saflufenacil and good post-emergence herbicidal activity at 37.5-150 g of ai/ha. Among these analogues, ethyl 2-((((2-chloro-4-fluoro-5-(3-methyl-2,6-dioxo-4-(trifluoromethyl)-3,6-dihydropyrimidin-1(2)-yl)phenyl)amino)methyl)thio)acetate () ( = 11 nM), exhibited excellent weed control at 37.5-150 g of ai/ha and was safe for rice at 150 g of ai/ha, indicating that compound has the potential to be developed as a new herbicide for weed management in paddy fields. Additionally, our molecular simulation and metabolism studies showed that the side chains of compound could form a hydrogen-bond-mediated seven-membered ring system; substituting a methyl group at R could reinforce the hydrogen bond of the ring system and reduce the metabolic rate of target compounds .