A data protection method for a memory storage apparatus is provided. The method includes obtaining a current system time from a host system as a boot time, if the memory storage apparatus is powered on, and a basic input/output system of the host system loads and executes instruction programs in the expansion ROM of the memory storage apparatus for transmitting the current system time to the memory storage apparatus. The method also includes obtaining a shutdown time corresponding to the memory storage apparatus; calculating an off time from the shutdown time to the boot time and performing a refresh operation on physical erasing units of a rewritable non-volatile memory in the memory storage apparatus if the off time is longer than an off time threshold.