To solve pollution problems caused by electromagnetic waves, advanced three-dimensional (3D) honeycomb Ag/Ti3C2Tx hybrid materials were produced by a microwave hydrothermal method. The Ag/Ti3C2Tx hybrid materials retained their hollow sphere structure after the polymethyl methacrylate (PMMA) template was removed by annealing. The hybrid materials changed from hydrophilic to hydrophobic and exhibited cross-surface heat insulation and reflection-dominant electromagnetic interference shielding (EMIS) performance owing to their special honeycomb structure. This study innovatively explored the influence of different particle sizes of honeycomb holes on EMIS performance. In particular, the Ag/Ti3C2Tx 5 μm hybrid materials had an excellent average EMIS performance of 51.15 dB in the X-band and 56.64 dB in the Ku-band. The superior performance was due to conduction loss, interface polarization, multi-reflection, and scattering caused by the 3D porous structure of the Ag/Ti3C2Tx hybrid materials. In general, Ag/Ti3C2Tx hybrid materials with honeycomb structures retained the advantages of lightweight, hydrophobicity, and EMIS performance, illustrating the great application prospects of these materials in high-end electronic equipment.