The invention relates to a gene for regulating the synthesis of flavonoids, its coded protein and its application, and belongs to the technical field of plant genetic engineering. The gene regulating flavonoid synthesis, the sequence is shown in SEQ ID NO: 1, which is derived from common tobacco, named NtMYB27, the NtMYB27 gene is 1240bp in length, contains 3 introns and 4 exons, and its coding region is complete 597 bp long. The present invention finds that the NtMYB27 transcription factor can inhibit the synthesis of flavonols in leaves through cloning analysis of gene sequences, construction of expression vectors, and gene expression detection, and this inhibition is achieved by inhibiting the expression of NtFLS and NtCHS genes of. Therefore, the present invention confirms that NtMYB27 is a negative regulator of plant flavonol synthesis. When the expression of this gene is inhibited or its function is lost, it can significantly increase the content of flavonols in plant leaves, providing a basis for the subsequent use of gene editing technology to enhance plant flavonols. Assays provide clear target genes.