Self-assembly technology is a promising strategy for improving the effective utilization of pesticides and reducing risks to the environment. Herein, four dimeric prodrugs were prepared by conjugating carfentrazone (CAR) with alkyl diols or dithiol and subsequently self-assembling into nanoparticles (CP NPs) through noncovalent forces without using any harmful adjuvant. The particle size of CP NPs with diols as linkers was negatively correlated with the linker carbon chain length, while that of 1,2-ethanedithiol-based CP NPs was smaller than those with ethylene glycol due to its stable bond angle structure. The obtained CP NPs exhibited superior herbicidal activities compared to the commercial formulation of CAR in both the greenhouse and field due to the improved physicochemical properties. In addition, CP NPs were safe to wheat and maize seedlings and had no effect on soil enzyme activity. Therefore, the proposed self-assembly strategy of dimeric prodrugs offers a promising pathway to improving pesticide efficiency while minimizing environmental risks.