A method of storing system data, and a memory controller and a memory storage apparatus using the same are provided. The method includes determining whether the unused storage space of a system physical erase unit is enough for storing updated system data. The method further includes, if the unused storage space of the system physical erase unit is not enough for storing the updated system data, selecting an empty physical erase unit, writing the updated system data into at least one first physical program unit of the selected physical erase unit and writing dummy data into a second physical program unit of the selected physical erase unit.