This paper addresses the issues of low transmission efficiency and poor misalignment tolerance in wireless power transfer for cardiac pacemakers. We propose a wireless power transfer system based on dual-layer magnetic negative (MNG) metamaterials and amorphous nanocrystals. The design leverages the high magnetic permeability and low loss characteristics of amorphous nanocrystals, along with the loss tangent and magnetic loss of the MNG. We conduct system performance and misalignment simulations at 6.78 MHz, demonstrating the system’s efficiency and stability. Comparative experiments between the dual-layer MNG and amorphous nanocrystal system, a traditional system, an amorphous nanocrystal system, and a dual-layer MNG system reveal that the combined dual-layer MNG and amorphous nanocrystal system achieves the highest output power and transmission efficiency of 2.09 W and 82.5%, respectively, when the transmitter (Tx) and receiver (Rx) are 20 mm apart. Furthermore, even with a 20 mm horizontal misalignment, the system maintains an output power of 1.58 W and a transmission efficiency of 62.4%, confirming the superior misalignment tolerance of the dual-layer MNG and amorphous nanocrystal system.