A method of protecting data in the cache memory of a storage system is used to protect the data stored in the cache memory of a first storage system and a second storage system coupled together and with the battery backed function. When the first storage system and the second storage system function normally, the data in their cache memory are mutually backed up. When any of the storage system has a power failure situation, the other normal storage system takes over the malfunctioned storage device. The data in its own cache memory are protected using the battery backed function. After the malfunctioned storage system restarts, the two storage systems keep backing up the data in the cache memory of each other. This provides a thorough protection of the data in the cache memory of the storage systems, increasing the reliability thereof.