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Floquet theory combined with the generalized Van Vleck nearly degenerate perturbation theory, has been widely employed for studying various two-level systems that are driven by external fields via the time-dependent longitudinal (i.e., diagonal) couplings. However, three-level systems strongly driven by the time-dependent transverse (i.e., off-diagonal) couplings have rarely been investigated, due to the breakdown of the traditional rotating wave approximation. Meanwhile, the conventional perturbation theory is not directly applicable, since a small parameter for the perturbed part is no longer apparent. Here we develop a double-unitary-transformation approach to deal with the periodically modulated and strongly driven systems, where the time-dependent Hamiltonian has large off-diagonal elements. The first unitary transformation converts the strong off-diagonal elements to the diagonal ones, and the second enables us to harness the generalized Van Vleck perturbation theory to deal with the transformed Floquet matrix and also allows us to reduce the infinite-dimensional Floquet Hamiltonian to a finite effective one. For a strongly modulated three-level system, with the combination of the Floquet theory and the transformed generalized Van Vleck perturbation theory, we obtain analytical results of the system, which agree well with exact numerical solutions. This method offers a useful tool to analytically study the multi-level systems with strong transverse couplings.