The improved relaxation approach of Meyer and co-workers is extended by employing the multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) theory. Within this approach the trial wave function is expressed by a recursive, multilayered expansion that is the same as in a normal ML-MCTDH simulation. Calculation of an energy eigenstate then proceeds by iteratively diagonalizing the Boltzmann operator in the top layer representation using a Lanczos/Arnoldi method while relaxing the single particle functions of all layers using the ML-MCTDH imaginary time propagation. Numerical iteration is stopped until the relative energy and/or density of the target state meet the convergence criteria. The application of this multilayer improved relaxation method is illustrated by computing the energy splitting for the lowest pair of eigenstates as well as the spin observables and entanglement entropy of the spin-boson model. A large number of degrees of freedom, up to 10 000 bath modes, can be treated, and thus the appropriate phase transition at a critical system-bath coupling strength may be predicted via appropriate extrapolations.