Hidden hunger caused by imbalanced human diet and lack of micronutrients has been paid increasing attention. One solution in achieving biofortification and functional food is to breed excellent crop varieties rich with various micronutrients by deployment of biological breeding technologies. A large number of studies have shown enrichment of anthocyanin, iron, zinc, selenium, trace nutrients and vitamins, folic acid, protein in color wheat germplasm resources. These components have certain effect for treatment of inflammation, cancer, diabetes, cardiovascular disease, anemia, and poor growth and development, etc, thus showing an important role in ensuring food security and human health. In this paper, we first introduce the background information of hidden hunger, biofortification, functional food, functional agriculture and functional varieties, followed by a highlighted summarization on the research progress of functional nutrition components and genetic breeding of colored wheat germplasm resources. We suggest to collect and create new color functional nutrition wheat germplasm, explore genes with excellent nutritional components, reveal the genetic coupling mechanism among anthocyanins and micronutritions (trace elements such as selenium, zinc and chromium, vitamins, 8 amino acids that cannot be synthesized by human body), in order to provide theoretical basis and technical support for color wheat biofortification and main grain functionalization.