Lilium concolor var. pulchellum has a brilliant flower colour, high germination rate, and resistance to cold, drought, and salinity and is an excellent source of lily germplasm. Anthocyanins are important flavonoids commonly found in plants and can make the flowers and fruits of plants more colourful. We first found that 0.2 mg/L 1-naphthaleneacetic acid (NAA) specifically induced the accumulation of anthocyanins, which were mainly cyanidins, in callus tissue culture of Lilium. Transcriptomic results indicated that anthocyanin accumulation was mainly involved in the flavonoid pathway, and an LhMYB1 transcription factor encoding 267 amino acids positively associated with anthocyanin accumulation was cloned from the MYB family. Subcellular localisation in tobacco showed that the gene was located in the nucleus of epidermal cells. Virus-induced gene silencing showed that silencing of the LhMYB1 gene on lily petals resulted in a purple to white colour change and a decrease in anthocyanin deposition, mainly in the upper and lower epidermis of the petals. Therefore, the results of this study will provide some ideas for the molecular breeding of lily flower colour.