A battery protection system applicable to an electronic device includes a battery, a control module, a message generating module and an input interface. The control module is electrically connected to the battery for detecting if the battery is in an abnormal state. The message generating module is electrically connected to the control module for generating a battery-error warning message when the control module detects that the battery is in the abnormal state. The input interface is electrically connected to the control module for transmitting a user command to the control module after the battery-error warning message is generated, thereby enabling the control module to release the abnormal state of the battery according to the user command. A battery protection method is also provided.