This study presents a novel pneumatic seed-metering device for precision soybean breeding, engineered to deliver two seeds per hill with high operational reliability. Its design features a compartmentalized structure and an integrated seed-clearing mechanism, explicitly addressing the key limitations of conventional seeders, such as low automation levels and intervarietal contamination during seed switching. The seed-metering and clearing processes were analyzed using coupled discrete element method–computational fluid dynamics (DEM–CFD) simulations. The exploratory DEM–CFD analysis identified distinct operational thresholds for seeding failures: miss-seeding occurred at disc rotational speeds exceeding 2.55 rad s⁻¹, while multiple-seeding issues were frequent at applied vacuum pressures above 5.6 kPa. Following this, a Central Composite Design (CCD) experiment was conducted in a controlled laboratory setting to examine the effects of operational speed and vacuum pressure on seeding quality indices. A multi-objective numerical optimization identified an optimal operational compromise with a seed-metering disc speed of 2.65 rad s⁻¹ (approximately 1.82 km h⁻¹) and an applied negative pressure of 5.80 kPa. This operating point effectively balances the competing failure modes of multiple seeding and miss-seeding, resulting in rates of 2.95% and 0.85% respectively. Field validation in saline–alkali soil conditions confirmed the device’s high precision, with actual multiple and miss-seeding rates maintained below 2% and 0.5%, respectively. Overall, this device significantly enhances seeding efficiency and operational reliability, providing a practical and effective solution for high-throughput soybean breeding programmes.