Provided are a charging system, a protection method and a power adapter. The charging system comprises: a battery, a first rectification unit, a switch unit, a transformer, a second rectification unit), a voltage sampling circuit, a control unit, and a comparator unit. The first rectification unit outputs the voltage with the first pulsating waveform. The switch unit outputs the modulated voltage with the first pulsating waveform. The transformer outputs the voltage with the second pulsating waveform. The second rectification unit outputs the voltage with the third pulsating waveform. The control unit adjusts a duty cycle of a control signal, such that the voltage of a third pulsation waveform meets the charging requirement of the battery. The comparator unit applies a comparison signal to the switch unit when the voltage sampling value is greater than the reference voltage value, so as to control the switch unit to forcibly open.