Modeling and amplification of erbium–ytterbium co-doped phosphate glass waveguide amplifier with a cascaded multilayer medium thin film filter is investigated theoretically. This proposed filter consists of some different filtering unit cells with different central wavelength and bandwidth, and each cell can suppress certain peak gain at a specific wavelength. The intrinsical gain spectrum of amplifier is obtained by solving a set of rate and power propagation equations, the effect of transmittance spectrum of thin film filter on flattening gain is discussed, and the transmission function of cascaded multilayer medium thin film filter is obtained.