The invention discloses an identity anti-counterfeiting system based on a quantum secret key and application thereof. The system comprises a main server S0, the server is in signal connection with n sub-servers Si (i belongs to 1, 2,..., n), each sub-server is provided with m (m > n) clients Cij (i belongs to 1, 2,..., n, j belongs to 1, 2,..., m), the main server S0 and the sub-servers Si share K entangled state particle pair sequences P, and the K entangled state particle pairs T are shared between the sub-server Si and the client Cij. According to the method, the lower level sends one particle in the EPR entanglement pair to the upper level, the other particle is reserved, an eavesdropper cannot obtain information of the whole EPR entanglement pair from one particle, during user authentication, a counterfeit client cannot know a secret key string between clients, particle measurement cannot be carried out according to a measurement base corresponding to a shared string, and therefore, the anti-counterfeiting effect is achieved.