In the paper, a wireless charger with the function of auto-shutdown for fully implantale middle ear hearing devices (F-IMEHD) has been designed. The wireless charger can communicate with an implant module to be turned off automatically shutdown after an internal rechargeable battery has been fully-charged by electromagnetic coupling using two coils. For the communication with an implant module, the wireless charger uses the load shift keying (LSK) method. But, the variation of the mutual inductance due to the different distance between two coils can cause the communication error in receiving the fully-charged signal from an implant module. To solve the problem, the implemented wireless charger has a variable reference generator for LSK communication. The wireless charger generates proper level of the reference voltage for a comparator using an ADC (analog-to-digital converter) and a DAC (digital-to-analog converter). Through the result of experiment, it has been confirmed that the presented wireless charger can detect signals from implantable module. And wireless charger can stop generating electromagnetic flux after an implanted battery has been fully charged in spite of variable coil distance according to different skin thickness.