Vanadium-bearing muscovite is the most valuable component of stone coal, which is a unique source of vanadium manufacture in China. Numbers of experimental studies have been carried out to destroy the carrier muscovite’s structure for efficient extraction of vanadium. Hence, the vanadium location is necessary for exploring the essence of vanadium extraction. Although most infer that vanadium may substitute for trivalent aluminium (Al) as the isomorphism in muscovite for the similar atomic radius, there is not enough experimental evidence and theoretical supports to accurately locate the vanadium site in muscovite. In this study, the muscovite model and optimal location of vanadium were calculated by density functional theory (DFT). We find that the vanadium prefers to substitute for the hexa-coordinated aluminum of muscovite for less deformation and lower substitution energy. Furthermore, the local geometry and relative electronic properties were calculated in detail. The basal theoretical research of muscovite contained with vanadium are reported for the first time. It will make a further influence on the technology development of vanadium extraction from stone coal.