Dianthus chinensis L. is an edible, ornamental herb used to prepare the Dianthi Herba, a Chinese traditional rejuvenating medicine. Owing to the rapid proliferation of callus tissues, in vitro production of flavonoids has their own specific importance. Callus cultures raised followed by auxin directed biosynthesis of flavonoid through related transcript profile were carried out. Murashige and Skoog (MS) medium fortified with 2,4- Dichlorophenoxy acetic acid (2,4- D) or picloram induced formation of friable callus from internode derived cultures of D. chinensis. Culture medium containing 2,4- D (10 µM) produced the highest flavonoid content, 4.44 mg quercetin equivalent per gram (QE g− 1) under incubation in continuous dark condition, while maximum dry weight yield (0.38 g/ culture) was obtained from 10 µM 2,4- D under 16 h light / 8 h dark condition (50 µmol m− 2 s− 1 irradiance) at 60 days of incubation. The callus raised in light condition in 10 µM 2,4- D selected to analyze flavonoid related gene expression profile viz., chalcone synthase (CHS), chalcone isomerase (CHI), flavanone-3-hydroxylase (F3H), and flavonol synthase (FLS) at specific time intervals. The transcript abundance of CHS, F3H, or FLS gene was higher at 60 days old callus cultures and reaching 11.59, 48.31, and 114.63-fold relative expression than that of initial callus tissues respectively. These understandings are critical for the regulation of targeted phytochemicals as well as their wide exploitation in the field of biological research.