A relevant pathway to meet future food production targets involves closing existing yield gaps, i.e., the difference between yields in researcher-managed trials and smallholder fields, through the adoption of technology. However, despite the availability of more productive and sustainable technologies, adoption remains low, and yield gaps persist. Understanding why smallholders fail to achieve high yields and how their productivity can be improved is crucial. To answer these issues, the soybean cropping system of Northeast China was selected as a case study. This is the first time that a generalizable framework that integrates crop modelling, long-term experimental data, statistics, and field surveys is proposed to map soybean yield gaps under various spatial scales (commercial farms, county, prefecture, and surveyed smallholders) and explain underlying causes. Pathways to bridge yield gaps are discussed. Compared with yield of researcher-managed experimental plots, soybean yields decreased from the farm to the county and again to the prefecture levels. At farm level, the yield gap was 0.34 t/ha, at county level 1.03 t/ha, and at prefecture level 1.17 t/ha. In the same order, a technical efficiency index decreased from 0.91 to 0.64. Poor agronomic management contributed to 73–86% of yield gap, followed by climate (26–13%) and soil constraints (less than 1%). Survey data showed that ridge planting pattern, the use of single compound fertilizers, and variety selection were the most important manageable variables affecting smallholder soybean yield. Using large-ridge cultivation and a rational application of fertilizers were critical for smallholders to achieve high yields. These findings suggest that bridging yield gaps in smallholder farming in the Northeast China remain a significant opportunity to improve food production. This study provides detailed information for closing yield gaps in smallholder fields. The framework is also applicable in other regions dominated by smallholder agriculture to develop sustainable intensification of production.