Abstract: In response to the prevalent challenges of high shellfish breakage rate, excessive sediment inclusion, and severe substrate compaction associated with conventional harvesting equipment for the subtidal Manila clam (Ruditapes philippinarum), this study designed and optimized a novel rotary-cutting harvesting apparatus. The research commenced with a critical analysis of the limitations of existing shallow-sea shellfish harvesting equipment—including drag-harrow, hydraulic, rotary-tooth, submerged-paddle, and vibration types—with particular emphasis on the adverse environmental impacts of hydraulic methods, such as sediment resuspension and nutrient release which can lead to eutrophication. Through systematic design and theoretical analysis, the trajectory of the harvesting blade was meticulously modeled, and key operational parameters, including the velocity ratio (λ), soil-cutting interval (S), and ridge height at the furrow bottom (Hc), were calculated to establish a theoretical foundation for the kinematic optimization. Factors influencing the sliding-cutting angle of the blade edge were thoroughly investigated, identifying the blade edge radius, bending angle, and width as the primary design variables. A high-fidelity simulation model was subsequently established using the Discrete Element Method (EDEM), wherein the intrinsic parameters of the substrate and clams were critically defined based on calibrated contact models, incorporating key sediment properties such as moisture content, bulk density, and internal friction angle. Using the blade edge radius, bending angle, and width as experimental factors, and the harvesting tool resistance and clam yield as the evaluation indicators, simulation results demonstrated that the optimal digging performance was achieved with an edge radius of 142 mm, a bending angle of 54°, and a blade width of 57 mm. Building upon these optimized blade parameters, a rotary-cutting harvesting mechanism was designed. Further simulation and Response Surface Methodology (RSM) analysis were conducted to determine the optimal operational parameters. The results indicated that the optimal harvesting performance was achieved with a forward speed of 0.6 m/s, a blade shaft speed of 125 r/min, and a blade spacing of 26 mm. Under these conditions, the clam harvesting rate reached 90%, with a mechanical load of 7.16 N exerted on individual clams and a total mechanism resistance of 476.26 N. A bench-scale test platform was constructed to validate the effects of forward speed, blade shaft speed, and blade spacing on harvesting performance and to verify the optimal operational parameters. The experimental results showed a harvesting rate of 93% and a blade shaft torque of 9.88 N·m. The relative errors between the bench test results and the simulation predictions were 3.33% for the harvesting rate and 5.40% for the shaft torque, confirming the reliability and accuracy of both the harvesting apparatus and the simulation model. A comprehensive comparative performance evaluation demonstrated the significant advantages of the proposed rotary-cutting apparatus over traditional hydraulic harvesting methods. Specifically, the sediment inclusion rate in the harvested clams was reduced by 61.49%, and the clam breakage rate was substantially lowered by 74.59%. Furthermore, the harvesting efficiency saw a notable improvement of 27.40%. From an ecological perspective, post-harvest substrate compaction measurements showed a 33.53% reduction compared to pre-harvest conditions, indicating a significantly minimized impact on the seabed ecosystem and promoting sustainable harvesting practices by adhering to the "catch-large-retain-small" principle. In conclusion, this study demonstrates that the designed rotary-cutting harvesting apparatus effectively addresses the critical issues of high breakage rate and sediment inclusion in Manila clam harvesting. It successfully achieves a harmonious balance between high harvesting efficiency and minimal environmental disturbance. The research outcomes, including the optimized structural and operational parameters and the validated simulation approach, provide valuable theoretical guidance and a practical reference for the design optimization and development of efficient and eco-friendly mechanized harvesting equipment for subtidal shellfish resources.