Profitability, Rather than Yield Alone, Limits Soybean Production in China

China is the world’s largest soybean consumer, yet persistently low domestic yields and weak economic returns limit supply. Current efforts mainly focus on technology, but the factors influencing yield and profitability under real farm conditions remain poorly understood. Here, we integrate 609 farmer surveys with machine learning and optimization techniques to identify the coupled biophysical and socioeconomic factors across China’s two major production regions, using Heihe and Jining as the representative cities in Northeast China and Huang-Huai-Hai Plain. We show that soybean performance is shaped by both biophysical and socioeconomic factors. Education consistently influences yield in both regions, while farm size plays a significant role in Jining. Despite similar yields (2.85 vs. 2.87 Mg ha−1), the determinants differ: In Heihe, performance is mainly influenced by variety, pesticide, herbicide and cropping patterns, whereas in Jining it is driven by precipitation, mechanization, temperature and irrigation. Profitability differs markedly, with higher net returns in Jining (4640 CNY ha−1) compared to Heihe (2030 CNY ha−1), reflecting structural differences in prices and land rental costs. Optimization results suggest that coordinated management improvements could increase profits by 1142 to 1859 CNY ha−1. Overall, the findings highlight that profitability, rather than yield alone, is the primary constraint shaping soybean systems, providing a data-driven framework for region-specific optimization and policy design.