The invention relates to a method for improving the reliability of a relay protection apparatus. The method comprises: pre-implanting a security program in a memory storing new files in the relay protection apparatus; when the new files are input into the apparatus through an external debugging computer, generating feature codes of the new files through the security program; matching virus feature codes in the security program with the feature codes of the new files one by one; performing security detection and judgment, isolating unsafe new files, and feeding judgment results back to the debugging computer through a CPU sending out a calling instruction; and displaying the corresponding judgment result by the debugging computer, and prompting whether an operation is successful or not for debugging personnel. According to the method, the hidden trouble caused by implantation of malicious programs or files after the apparatus is put into operation is avoided, the reliability of the apparatus is further improved, the probability of accidents in operation is reduced, and meanwhile important guidance is provided for the debugging personnel in whether the new files are secure or not and whether the new files are input successfully or not.