The coaxiality of the transmitter and receiver has a significant impact on the efficiency in a wireless power transfer system. In order to keep high system efficiency, a novel coil structure is studied in this paper. Several plane coils are crossed to make up a three-dimensional coil structure in the transmitter, which will make sure the system in the state of strong magnetic field coupling. In the theory part, the magnetic field equation of different relationships between transmitter and receiver is deducted in detail. In the simulation part, the performance of the three-dimensional coil structure has been studied. The simulation results show that the new coil structure can generate a rotating magnetic field, and the rotating magnetic field will keep the system in the state of the strong magnetic field coupling in the simulation model. In the experimental part, the three-dimensional coil structure has been compared to a plane coil structure. The experimental results show that the efficiency of the three-dimensional coil structure is increased above 10% in the misalignment situation. The simulated and experimental results show that the new three-dimensional coil structure has a better performance in the misalignment situation than the plane coil structure in a wireless power transfer system.