The non-equilibrium thermo-field dynamics formulation of the hierarchical equations of motion combined with the tensor-train representation of the density matrix is discussed, and a new numerical integration scheme is introduced. The numerical methodology is based on an adaptive low-rank Galerkin reduction scheme and can preserve linear invariants (such as the trace of the density matrix). The method is applied to the study of the charge transfer dynamics in model pentacene molecular aggregates. The combined effect of a discrete set of molecular vibrational modes and a thermal bath is investigated, paying special attention to the coherent-incoherent transition of the charge transport. The new computational framework is shown to be a very promising methodology for the study of the quantum dynamics of complex molecular systems in the condensed phase.