We extend the multiconfiguration time-dependent Hartree-Fock (MCTDHF) theory, which is originally developed for the investigation of electronic dynamics in atoms and molecules within the clamped nuclear model, for describing molecular dynamics in diatomic-like molecular systems which are composed of electrons, protons, and two heavy nuclei such as CH(3)OH, C(2)H(2), C(2)H(4), and H(5)O(2) (+). A novel representation of the molecular (electrons and nuclei) wave function to describe the electronic and nuclear quantal dynamics of molecules in an intense laser field is proposed, and the explicit coupled equations of motion (EOMs) for electron spin-orbitals, proton spin-orbitals, and CI-vectors are formulated. The CI-vectors are introduced to describe the quantal motion of the internuclear distance between two heavy nuclei. The derivation of the EOMs is done in two steps. First, the distance between the two heavy nuclei R is treated classically, i.e., electro-protonic dynamics within the clamped nuclear model, and then, the distance R is treated quantum mechanically to describe non-Born-Oppenheimer molecular dynamics. The properties of the EOMs are discussed for the application of the present theory to clarify the mechanism of intramolecular hydrogen (proton) migration processes within hydrocarbon molecules competing with the ionization and the fragmentation processes in intense laser fields.