A multilayer (ML) formulation of the multiconfiguration time-dependent Hartree (MCTDH) theory is presented. In this new approach, the single-particle (SP) functions in the original MCTDH method are further expressed employing a time-dependent multiconfigurational expansion. The Dirac-Frenkel variational principle is then applied to optimally determine the equations of motion. Following this strategy, the SP groups are built in several layers, where each top layer SP can contain many more Cartesian degrees of freedom than in the previous formulation of the MCTDH method. As a result, the ML-MCTDH method has the capability of treating substantially more physical degrees of freedom than the original MCTDH method, and thus significantly enhances the ability of carrying out quantum dynamical simulations for complex molecular systems. The efficiency of the new formulation is demonstrated by converged quantum dynamical simulations for systems with a few hundred to a thousand degrees of freedom. (C) 2003 American Institute of Physics.