First, [(1-x)MnO2-xMWCNTs] (MMCs) nanocomposites and modified [(1-x)MnO2-xMWCNTs] (mMMCs) nano- composites were synthesized. Then, novel modified [(1-x)MnO2-xWCNTs]/waterborne polyurethane (mMMCs/WPU) composites with good microwave absorption properties were prepared by in situ polymerization. The chemical functionalized MMCs and mMMCs nanocomposites were characterized by FTIR and XRD. The structure and properties of the mMMCs/WPU composites were investigated by SEM, TGA, tensile testing, and vector network analyses. The experimental results showed that when the mMMCs nanocomposites were introduced into WPU the thermal stability and tensile strength of mMMCs/WPU composites were improved. When the content of MWCNTs was 20 wt % (where x = 0.2), m[(1-x)MnO2-xMVVCNTs]/WPU composites exhibited good microwave absorption properties. The minimum RL value can reach -28.7 dB at 6.4 GHz with a thickness of 2.5 mm. The mMMCs/WPU composites have good thermal stability and tensile strength, which could be used as promising materials for microwave absorption.