Flavonoids are secondary metabolites widely distributed in plants. They not only confer a wide spectrum of pigmentation to plant flowers but also protect plants from various biotic and abiotic stresses. Simultaneously, these compounds also offer health benefits to humans. Significant efforts have been made to correlate specific flavonoid production with biosynthetic pathway gene expression. Some structure genes and transcription factors that regulate the biosynthetic pathway have been identified. However, the diverse and complex control of flavonoid accumulation is still not well understood. In this mini-review, we summarized the improvement of flavonoids by genetic engineering from the aspects of flower colour, plant resistance, and benefits on the human diet. A perspective on flavonoid research in plants is provided.