Background and aims <p>Manual separation of bare seedlings for peony planting is a challenging issue in the industry due to high labor consumption and low productivity. The study focuses on the interaction relationships between seedling-seedling and mechanism-seedling as well as the separation mechanism within a vibration field, aiming to provide new ideas for automated peony transplanting.</p> Methods <p>Firstly, based on the vibration characteristics of materials, a flexible vibration platform is designed, and a virtual prototype model of the mechanism is established. The optimization of flexible mechanism parameters for achieving multi-mode vibration is then conducted. Subsequently, through studying the morphological characteristics of bare peony seedlings, the stages of seedling separation are defined, and a multi-mode vibration seedling separation method is determined using analytical analysis. This separation involves seedling cluster throwing motion for dispersion and sliding motion for separation.Simulation analysis reveals the inherent relationship between device structural parameters, operation parameters, and the degree of seedling separation.</p> Results <p>Field test results show that, with a throwing frequency of 14.4 Hz, a sliding frequency of 7.7 Hz, the highest success rate of peony seedling separation is 87.6%, which can adequately meet agricultural production needs.</p> Conclusion <p>This research provides a theoretical basis and methodological support for developing automatic seedling separation equipment for peonies or other elongated bare seedlings.</p>