The invention discloses an EID security control method and system based on eID. The system comprises a virtual identity management system VIMS and an EID management system EMS of a target application system AS, wherein the VIMS is used for authenticating a user; if authentication is passed, a binding request is generated, and sent to the EMS; when the user accesses the AS, a login request is generated, and sent to the EMS; the EMS is used for authenticating the user according to the binding request; if authentication is passed, the Ie of the eID identity of the user is returned; then, the Ie is bound with account numbers Iv and V included in the binding request; then, a binding result is sent to the VIMS; the user is authenticated according to the login request; if authentication is passed, authentication result information is generated according to a returned virtual account number set {I} and the identifier E of the EMS, and returned to the VIMS; and the VIMS obtains the virtual account number Iv included therein, and processes access of the user.