The fractional non-isotropic \(n\) -dimensional modified Stockwell transform (FNIMST) is introduced as a novel time-frequency analysis tool that extends both the classical Stockwell transform and the fractional Fourier transform. This paper establishes the fundamental properties of the FNIMST, including its basic characteristics, inversion formula, and key inequalities. Several uncertainty principles (UPs) are derived, including the weak uncertainty principle, Lieb’s uncertainty principle, and the local uncertainty principle. The study also explores the concentration properties of the FNIMST in sets of finite measure, leading to a Shapiro-type dispersion theorem.