Staphylococcus aureus (S. aureus)-infected osteomyelitis is a deep tissue infection that cannot be effectively treated with antibiotics. Microwave (MW) thermal therapy (MTT) and MW dynamic therapy (MDT) based on MW-responsive materials are promising for the therapy of bacteria-infected osteomyelitis occurring in deep tissues that cannot be effectively treated with antibiotics. In this work, the MW-responsive system of carbon nanotubes (CNTs)/Prussian blue (PB)/puerarin (Pue) with stable network-like structures is constructed. The PB is grown in situ on the CNTs, and its introduction not only reduces the aggregation of the network-like structures of the CNTs, but the large specific surface area and mesoporous structure can also provide many active sites for the adsorption of oxygen and polar molecules. Pue is a natural anti-inflammatory material that reduces inflammation at the infection site. The composite of the CNTs and PB avoids the skin effect and thus can improve dielectric and reflection losses. The MW thermal response of CNTs/PB/Pue is mainly due to the occurrence of reflection loss, dielectric loss, multiple reflections and scattering, interface polarization, and dipole polarization. In addition, under MW irradiation, the CNTs/PB/Pue can produce reactive oxygen species (ROS), such as singlet oxygen (1O2), hydroxyl radical (·OH).