A considerable number of waveguide multiplexer are installed to combine channel signals in communication satellite. Especially, Ku band multiplexer is a key component to realize communication payload due to its large function. A demand of the Ku band multiplexer according to communication system is combining not only a lot of channels but also variety and complicated frequency arrangement of the channels with several bandwidths. Therefore, a suitable design method is necessary to facilitate the design of multiplexer requirement. This paper proposes new design method that can easily realize a wavegude multiplexer with the complicated arrangement of the channels. To begin with, two kinds of BPF coupling coefficients of contiguous and non-contiguous channels are used for the initial values of complicated multiplexer to decrease the parameters of multiplexer. Next, optimization will be done with only changing the length of the waveguide manifold. This simplified procedure has facilitated the optimization of multiplexer design with the complicated arrangement of the channels. Finally, fabrication and qualification test results of a waveguide output multiplexer for satellite application are shown.