The quantum phenomena of electronic and nuclear resonances are associated with structures in measured cross sections. Such structures were recently reported in a cold chemistry experiment of ground-state hydrogen isotopologues (H2/HD) colliding with helium atoms in the excited triplet P-state (He(23P)) [Shagam et al. Nature Chem. 2015, 7, 921], but a theoretical explanation of their appearance was not given. This work presents a quantum explanation and simulation of this experiment, which are strictly based on ab initio calculations. We incorporate complex potential energy surfaces into adiabatic variational theory, thereby reducing the multidimensional scattering process to a series of uncoupled 1D scattering "gedanken experiments". Our theoretical result, which is in remarkable agreement with the experimental data, manifests that the structures in the observed reaction rate coefficient are due to the spatial arrangement of the excited He p-orbitals with respect to the interaction axis, consequently changing the system from a normal two-rotor model to a three-rotor one. This theoretical scheme can be applied to explain and predict cross sections or reaction rate coefficients for any resonance-related phenomenon.