Abstract: To address the common issues of low fruit removal efficiency and poor adaptability in existing pecan mechanized harvesters, a hydraulically driven dual-drive counter-rotating differential vibration method for pecan harvesting operations was proposed. First, the overall structural design of a vibration-based shaker harvester suitable for large pecan trees was completed, and a coupled rigid-flexible dynamic vibration picking model was developed to simulate the interaction between the clamping-vibration component and the main trunk of the pecan tree. In this model, the clamping assembly was treated as a rigid body while the tree trunk was modeled as a flexible body, enabling detailed analysis of their coupled vibratory dynamics. Then, the variation patterns of excitation force under counter-rotating differential vibration were analyzed. The main factors affecting harvesting performance were identified as the base rotational speed for one of hydraulically driven motors, the differential rotation coefficient between the two hydraulically driven motors, and vibration duration applied to the pecan tree. Second, finite element simulation analysis software was adopted, and the structure and operation parameters of key parts of excitation and clamping were designed to enhance the system’s performance. Specifically, the geometry of the eccentric mass blocks was refined, including their structural configuration, eccentric offset distance, and mass moment of inertia, along with the structural parameters and material selection of the excitation main shaft. Additionally, the main parameters of the dual hydraulic drive motors and the design value of the clamping preload force were established. Finally, pecan picking machine was trial-produced, and based on the established picking test conditions and methods, a full-machine performance test was conducted. The results showed that, for mature pecan trees with trunk diameters of 35～45 cm, the optimal operating parameters were a base rotational speed of 1200 r/min, a rotational coefficient of 0.8 based on base speed, and a vibration duration of 7 seconds. Meanwhile, the harvester achieved a fruit picking rate of 88.8% in a single shaking pass per tree. In addition, verification of the overall harvesting performance under the optimal operating parameters showed that the average pecan picking rate was 85% in a single shaking pass per tree, with no destructive damage to the tree trunk. Meanwhile, the average harvesting efficiency was 40 trees per hour, approximately 16 times higher than that of manual harvesting. These results confirmed that the developed harvester met the mechanized harvesting requirements of pecan orchards and effectively addresses the shortcomings of existing harvesting equipment, particularly with respect to efficiency and adaptability.