We present a method that brings prediction of phase behaviors of various clathrate hydrates with firm statistical mechanical ground adopting a different reference state from the usual one. Accommodation of a large guest molecule makes the frequencies of the lattice vibrational motions higher, which is one of the breakdowns of the assumptions in the original van der Waals and Platteeuw theory. The frequency modulations are incorporated in the free energy of cage occupation in the present method. Moreover, the reference state, which is originally the corresponding empty clathrate structure, is alternated to a state where cages of at least one sort are fully occupied. This meets the stability condition of clathrate hydrates that most of the cages should be accommodated. Owing to this new reference state, the thermodynamic stability is evaluated with reasonable accuracy from the free energy of cage occupation especially by a large guest molecule without considering its dependence on the cage occupancy. This conversion is also beneficial to establish a relation between the chemical potential of water and the cage occupancy from grandcanonical Monte Carlo simulation. We show a new method indeed works well in predicting the dissociation pressures of clathrate hydrates containing isobutane, propane, ethane, Xe, and CF(4).