The creation of high-yielding varieties is a priority task for achieving the objectives of sustainable development, specifically in eradicating hunger and promoting good health and well-being for humanity. Automation of the breeding process requires expanding the capabilities of automated phenotyping. The issue of digital phenotyping of plants is the foundation for automating the breeding process. The creation of the system for the digital model of the Helianthus phenotype, which is used to implement selection programs for confectionery sunflowers, is chosen as a significant task. The work was carried out in cooperation with experts from the Institute of Oilseed Crops of the National Academy of Agricultural Sciences of Ukraine. The work results are the formalization of the concept of the Helianthus phenotype digital model and the structural scheme of the system for the digital model of the Helianthus phenotype (seed and head). In the course of work, software for image processing of confectionary sunflower seeds was developed using Python programming.