The microstructure height is one of the important parameters of Diffractive Optical Elements (DOEs). On the basis of the relationship of Polychromatic Integral Diffraction Efficiency (PIDE) with the microstructure heights of Double-layer Diffractive Optical Elements (DLDOEs), the optimal design method was analyzed and presented. Under the premise of satisfying the performance requirements of the optical system, the reduction of the microstructure height can be realized by reducing PIDE. The DLDOEs operating in the visible light band, long-wave infrared band and two infrared bands were simulated and analyzed respectively. The analytical results showed that the microstructure height of the DLDOE operating in the long-wave infrared band could be reduced by more than 55% when its 1.9% PIDE was sacrificed with this method. This conclusion was of great significance to the fabrication and application of DLDOEs.