The invention discloses an electromagnetic inductive type non-contact charging system and an aligning method thereof. The system comprises a ground electric energy emitting device and a vehicle-mounted electric energy receiving device, wherein the vehicle-mounted electric energy receiving device comprises a display module, a vehicle-mounted part controller, a vehicle-mounted wireless communication module, a vehicle-mounted electric energy receiving module, a battery and a vehicle-mounted receiving coil, and is arranged on a vehicle, the vehicle-mounted receiving coil is arranged below a chassis, the ground electric energy emitting device comprises a ground emitting coil, a ground electric energy emitting circuit, a driving module, a ground part controller and a ground wireless communication module, and is arranged on the ground, and the ground emitting coil is arranged on the top of the ground electric energy emitting device. On the basis of the traditional non-contact charging, a positioning aligning device taking the charging efficiency as the control target is added, so that an automatic optimizing function for the charging efficiency is realized; the system and the method are simple and easy to implement, and whether the current situation is suitable for charging or not can be judged only by monitoring the charging efficiency.