The widespread use of chemical herbicides has jeopardized concerns about food safety and ecological consequences. To address these issues and reduce reliance on chemical herbicides, a physical weed control device was developed for the tillering stage in paddy fields. This device features a biomimetic duckbill-like vibration chain that effectively controls weed outbreaks. The chain penetrates the soft surface soil of the paddy field under gravity and rapidly stirs the soil through vibration, leading to the detachment of the weed roots anchored in the surface layer. Simultaneously, the device avoids mechanical damage to rice seedlings rooted in deeper soil. This study aimed to investigate the effects of chain structural parameters (the number of chain rows, vibration amplitude, and length of chains) and operational parameters (vibration frequency and working velocity) on weed control efficiency and rice seedling damage. Through a central composite regression field test, the optimal device structure and operational parameters were determined. The optimization results demonstrated that a vibration amplitude of 78.8 mm, a chain length of 93.47 cm, and 3.4 rows of chains, along with a vibration frequency and working velocity ranging from 0.5 to 1.25 m/s, achieved an optimal weeding effect. Under the optimal parameter combination, field test results demonstrated that approximately 80% of the weeds in the field were effectively cleared. This indicates that the design of the biomimetic duckbill-like vibration chain weeding device exhibits a relatively superior weeding performance, offering a practical solution for the management of weeds in rice fields.