Prethermalization, where quasisteady states are realized in the intermediate long-time regime (prethermal regime), in periodically driven (Floquet) systems is an important phenomenon since it provides a platform for nontrivial Floquet many-body physics. In this Rapid Communication, we consider Floquet systems with dual energy scales: The Hamiltonian consists of two different terms whose amplitude is either comparable to or much smaller than the frequency. As a result, when the larger-amplitude drive induces a Z(N) symmetry operation, we obtain the effective static Hamiltonian respecting the emergent Z(N) symmetry in high-frequency expansions, which describes the dynamics of such Floquet systems in the prethermal regime. As an application of our formulation, our formalism gives a general way to analyze time crystals in prethermal regimes in terms of the static effective Hamiltonian. We also provide an application to Floquet engineering, with which we can perform the simultaneous control of phases and symmetries of the systems. For example, this enables us to control symmetry protected topological phases even when the original system does not respect the symmetry.