We developed an approximate method for quantum reaction dynamics simulations, namely, a structure-based Gaussian (SBG) expansion approach, where SBG bases for the expansion of the wave function Ψ, expressed by a product of single-atom Cartesian Gaussians centered at the positions of respective nuclei, are mainly placed around critical structures on reaction pathways such as on the intrinsic reaction coordinate (IRC) through a transition state. In the present approach, the "pseudo-lattice points" at which SBGs are deployed are selected in a perturbative manner so as to make moderate the expansion length. We first applied the SBG idea to a two-dimensional quadruple-well model and obtained accurate tunneling splitting values between the lowest four states. We then applied it to hydrogen tunneling in malonaldehyde and achieved a tunneling splitting of 27.1 cm-1 with only 875 SBGs at the MP2/6-31G(d,p) level of theory, in good agreement with 25 cm-1 by the more elaborate multiconfiguration time-dependent Hartree method. Reasonable results were also obtained for singly and doubly deuterated malonaldehyde. We analyzed the tunneling states by utilizing expansion coefficients of individual SBGs and found that 40-45% of the SBGs in Ψ are nonplanar structures and SBGs away from the IRC contribute a little to hydrogen transfer.