The invention discloses a public key protection method and a public key protection system of a security chip. The public key protection method comprises the following steps: before the public key operation is started, checking values of all initial values in the configuration register of the security chip are calculated and stored; after the public key operation is started, verifying the value inthe configuration register of the security chip in real time, and if the verification fails, terminating the operation and reporting an error. The public key protection method of the security chip candetect the fault attack of the whole flow of the public key algorithm module in real time without increasing the operation time of the public key algorithm.