We present a substrate material selection method for multilayer diffractive optical elements (MLDOEs) to obtain high polychromatic integral diffraction efficiency (PIDE) in a wide environmental temperature range. The extended expressions of the surface relief heights for the MLDOEs are deduced with consideration of the influence of the environmental temperature. The PIDE difference Δη¯(λ) and PIDE change factor F are introduced to select a reasonable substrate material combination. A smaller value of Δη¯(λ) or F indicates a smaller decrease of the PIDE in a wide temperature range, and the corresponding substrate material combination is better. According to the deduced relation, double-layer and three-layer DOEs with different combinations are discussed. The results show that IRG26 and zinc sulfide is the best substrate material combination in the infrared waveband for double-layer DOEs, and polycarbonate is more reasonable than polymethyl methacrylate as the middle filling optical material for three-layer DOEs when the two substrate materials are the same.