AbstractFor autogamous crops, a precondition for using heterosis is to produce sufficient pure male‐sterile female parents that can be used to produce hybrid seeds. To date, cytoplasmic male sterility (CMS) and environment‐sensitive genic male sterility (EGMS) have been used commercially to exploit heterosis for autogamous species. However, neither CMS nor EGMS has been established for foxtail millet (Setaria italica). Here, we report on the establishment and application of a seed production technology (SPT) system for this crop. First, we established a DsRed‐based SPT system, but found that it was unsuitable because it required the use of a fluorescent device for seed sorting. Instead, we constructed an SPT system with de novo betalain biosynthesis as the selection marker. This allowed us to distinguish transgenic seeds with the naked eye, thereby facilitating the identification of SPT maintainer line seeds. In this system, a seed sorter was not required to obtain sufficient seeds. The key point of the strategy is that the seed pool of the SPT maintainer line is propagated by artificial identification and harvesting of male‐fertile individuals in the field, and the male‐sterile line seed pool for hybrid production is produced and propagated by free pollination of male‐sterile plants with the SPT maintainer line. In a field experiment, we obtained 423.96 kg male‐sterile line seeds per acre, which is sufficient to plant 700.18 acres of farmland for hybrid seed production or male‐sterile line reproduction. Our study therefore describes a powerful tool for hybrid seed production in foxtail millet, and demonstrates how the SPT system can be used for a small‐grained crop with high reproduction efficiency.