In this article, we develop and analyse a new spectral method to solve the semi-classical Schr\"odinger equation based on the Gaussian wave-packet transform (GWPT) and Hagedorn's semi-classical wave-packets (HWP). The GWPT equivalently recasts the highly oscillatory wave equation as a much less oscillatory one (the $w$ equation) coupled with a set of ordinary differential equations governing the dynamics of the so-called GWPT parameters. The Hamiltonian of the $ w $ equation consists of a quadratic part and a small non-quadratic perturbation, which is of order $ \mathcal{O}(\sqrt{\varepsilon }) $, where $ \varepsilon\ll 1 $ is the rescaled Planck's constant. By expanding the solution of the $ w $ equation as a superposition of Hagedorn's wave-packets, we construct a spectral method while the $ \mathcal{O}(\sqrt{\varepsilon}) $ perturbation part is treated by the Galerkin approximation. This numerical implementation of the GWPT avoids imposing artificial boundary conditions and facilitates rigorous numerical analysis. For arbitrary dimensional cases, we establish how the error of solving the semi-classical Schr\"odinger equation with the GWPT is determined by the errors of solving the $ w $ equation and the GWPT parameters. We prove that this scheme has the spectral convergence with respect to the number of Hagedorn's wave-packets in one dimension. Extensive numerical tests are provided to demonstrate the properties of the proposed method.

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