This paper presents an optimizing method for wireless charging system, specifically focused on the capsule endoscope applications. In order to increase the wireless power transfer efficiency of electro-magnetic resonance coupled coils, this paper investigates the impact factors of the power transfer efficiency in small battery capacity system and proposes a efficiency optimizing method based on frequency control. Simulation results show that the proposed efficiency optimal control method can effectively stabilize the wireless power transfer efficiency so as to successfully solve the main issue of transfer efficiency variation with distance and as well as parasitic element.