We have developed a time-dependent multiconfiguration wave function theory for electronic dynamics of molecules within the Born-Oppenheimer approximation in intense laser fields. Recently, we have extended it to describe molecular dynamics in diatomic-like molecular systems which are composed of electrons, protons and two heavy nuclei. 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 for electron spin-orbitals, proton spin-orbitals and CI-vectors are derived. The CI-vectors are introduced to describe the quantal motion of the internuclear distance between two heavy nuclei. The properties of the EOMs will be 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 by showing the numerical results for the ground state wave function calculations for a methanol and a 1D hydrogen molecule.