The enzyme browning reaction results in grey speckles on tobacco leaves, which impairs the value and industrial usability of tobacco leaves. To demonstrate the influences of different browning degrees (BDs) of tobacco leaves on the usability of different cultivars and positions and identified structure of brown (grey) matter, we selected three flue-cured tobacco cultivars (K326, Yunyan87, and Honghuadajinyuan (Hongda)) and set four different BDs (<25%, 25% to 50%, 50% to 75%, and >75%). Indices related to: economic traits, chemical components, physical properties, and sensory quality of tobacco leaves with different cultivars were evaluated. Moreover, by utilising thin-layer chromatography and high-performance liquid chromatography, we analysed and identified the structure of the grey matter in terms of chemical composition. The experimental results show that the main component of grey speckles on tobacco leaves is 3-acetyl-6,7-dimethoxycoumarin (YC-ZJF). With the increase of BD, the amount of total sugar and reducing sugar, output value, the proportion of superior tobacco, shatter resistance index, and sensory evaluation score of the three cultivars significantly decrease, while the starch content increases significantly. The changes in protein, total nitrogen, and nicotine are insignificant with changing BD. In addition, other indices show different trends for different cultivars of flue-cured tobacco. After separation and identification of the components of grey speckled leaves, it is proved that the substance derived from grey speckles on tobacco leaves is YC-ZJF. The research is important to the study of browning mechanisms in tobacco leaves and provides corresponding targets for strategies to reduce browning thereof.