Improving the effective action by the renormalization group (RG) with several mass scales is an important problem in quantum field theories. A method based on the decoupling theorem was proposed in [1] and systematically improved [2] to take threshold effects into account. In this paper, we apply the method to the Higgs-Yukawa model, including wave-function renormalizations, and to a model with two real scalar fields (φ, h). In the Higgs-Yukawa model, even at one-loop level, Feynman diagrams contain propagators with different mass scales and decoupling scales must be chosen appropriately to absorb threshold corrections. On the other hand, in the two-scalar model, the mass matrix of the scalar fields is a function of their field values (φ, h) and the resultant running couplings obey different RGEs on a different point of the field space. By solving the RGEs, we can obtain the RG improved effective action in the whole region of the scalar fields.