A digital certificate issuing system with intrusion tolerance ability and the issuing method thereof are disclosed. The system comprises an offline secret key distributor, at least one online task distributor, k online secret share calculators and m online secret share combiners. And the method includes: splitting a private key into multiple first sub-secret-keys and multiple second sub-secret-keys, wherein the multiple first sub-secret-keys are divided into k groups, and the private key is constructed by one second sub-secret-key and t first sub-secret-keys, the second sub-secret-key corresponds to the t first sub-secret-keys according to an equation combination representation including t items of j and i, j is sequence number of the group which has the first sub-secret-key, and i is number of the first sub-secret-key in the jth group, each of j in one equation combination representation is different, j, i, k, and t are positive integers, and t is less than k; calculating t first calculation results according to a certificate to be signed and the t first sub-secret-keys in the multiple first sub-secret-keys upon receiving the certificate to be signed; obtaining the second sub-secret-key corresponding to the t first sub-secret-keys according to the equation combination representation; calculating a second calculation result according to the second sub-secret-key obtained and the certificate to be signed; generating a digital signature according to the t first calculation results and the second calculation result; generating a digital certificate according to the digital signature and contents of the certificate to be signed.