Increasing plant density is a key measure to close the maize (Zea mays L.) yield gap and ensure food security. However, there is a large plant density difference in the fields sown by agronomists and smallholders. The primary cause of this phenomenon is the lack of an effective methodology to systematically analyze the density loss. To identify the plant density loss processes from experimental plots to smallholder fields, a research methodology was developed in this study involving a farmer survey and measurements in a smallholder field. The results showed that the sowing density difference caused by farmer decision-making and plant density losses caused by mechanical and agronomic factors explained 15.5%, 5.5% and 6.8% of the plant density difference, respectively. Changing smallholder attitudes toward the value of increasing the plant density could help reduce this density loss and increase farm yields by 12.3%. Therefore, this methodology was effective for analyzing the plant density loss, and to clarify the primary causes of sowing density differences and plant density loss. Additionally, it was beneficial to identify the priorities and stakeholders who share responsibility for reducing the density loss. The methodology has wide applicability to address the sowing density differences and plant density loss in other areas to narrow crop yield gaps and ensure food security.