In recent years, electromagnetic shielding materials with low reflectance have developed rapidly. However, high material cost, poor bonding fastness, weak mechanical properties and other problems seriously limit its effect in practical use. In this work, flexible conductive collagen fibers (CLF-Zr4+/Al3+-CNTs) were prepared using chromium tanned waste leather as ingredient, carbon nanotubes (CNTs) as conductive filler and transition metal ions as coordination crosslinking agents, and their molecular dynamics were investigated by quantum chemical simulation software. On this basis, a flexible conductive foam with the double layer and double core-clad structure containing carbon nanotubes was constructed using the solvent-free polyurethane (SFPU) chemical foaming technology, and their electromagnetic shielding properties and reflectance were studied. The experiment results showed that when the ratio of CLF-Zr4+/Al3+-CNTs to SFPU polyol is 1:9 and the impregnation times of CNTs are 2, the loading capacity of CNTs in conductive foam is 0.14 mg/cm3, the electrical conductivity is 57.8 S/m, and the thermal conductivity is 0.061 W/(m·K). Meanwhile, when the thickness is 3 cm, the electromagnetic shielding performance is 42.09 dB, and the reflection efficiency is 0.66 %, the lowest reflection efficiency reaches 0.16 % in the experiment. The mechanism of electromagnetic shielding in conductive foams with the double layer and double core-clad structure has been further explored. The experiment results proved that the flexible conductive foam has excellent mechanical properties, stability, heat insulation and flame retardant properties, and has excellent electromagnetic shielding and low reflection characteristics due to its abundant holes, functional group, interface and hierarchical structure.