The invention provides a self-destroying protection method based on a malicious invasion of a file system. The method comprises the steps that when the content of a specified file in a common disk is not matched with the content in a specific file, the number of times of the malicious invasion of a hidden disk is accumulated; when the number of times of the malicious invasion of the hidden disk reaches an upper limit, the file system of the hidden disk is deleted, and the content in the hidden disk cannot be read. A device executing the method comprises a file type detection module, a content comparison module, an accumulating module, a comparison module for the number of times and a file system deleting module. The file type detection module is used for detecting the type of the specified file stored in the common disk of equipment, the content comparison module is used for distinguishing whether the content of the specified file is matched with that of the specific file or not, the accumulating module is used for accumulating the number of times of the malicious invasion of the hidden disk, the comparison module for the number of times is used for comparing the accumulated number of times of the malicious invasion of the hidden disk and the upper limit value of the accumulated number of times, and the file system deleting module is used for deleting information in an FAT area of the hidden disk. According to the method and the device, the safety of data in the equipment can be improved, and the data are effectively prevented from being illegally copied.