An electronic signature authentication system based on biometric information, comprising: an authentication server configured to register a public key of a signer (U PK) generated based on biometric information for user identification and perform authentication of an electronic document that is electronically signed with a private key of the signer (U SK) generated based on the biometric information, and that is verified by using the public key of the signer (S915-S940); an electronic document device configured to request an electronic signature for the electronic document to a user device, extract encryption data (E1-E4) from data received from the user device, and generate a final electronic file for storage by combining the encryption data (E2-E5) with the electronic document to transfer to the authentication server; and the user device configured to register the biometric information for user identification of the signer and a handwritten signature for document confirmation entered from the signer, generate the public key (U PK) and the private key (U SK) of the signer based on the registered biometric information for user identification (S130, S510), register the public key of the signer to the authentication server (S135, S515), receive a handwritten signature for document confirmation of the signer in response to a signature request from the electronic document device, determine whether the received handwritten signature for document confirmation matches the registered handwritten signature for document confirmation, complete the input of the handwritten signature in a signature field in the electronic document to be signed (S200-S210), generate an electronic signature value (DS1-DS3) by using the private key of the signer (U SK), and generate the encryption data (E1-E4) by encrypting the generated electronic signature value. an authentication server configured to register a public key of a signer (U PK) generated based on biometric information for user identification and perform authentication of an electronic document that is electronically signed with a private key of the signer (U SK) generated based on the biometric information, and that is verified by using the public key of the signer (S915-S940); an electronic document device configured to request an electronic signature for the electronic document to a user device, extract encryption data (E1-E4) from data received from the user device, and generate a final electronic file for storage by combining the encryption data (E2-E5) with the electronic document to transfer to the authentication server; and the user device configured to register the biometric information for user identification of the signer and a handwritten signature for document confirmation entered from the signer, generate the public key (U PK) and the private key (U SK) of the signer based on the registered biometric information for user identification (S130, S510), register the public key of the signer to the authentication server (S135, S515), receive a handwritten signature for document confirmation of the signer in response to a signature request from the electronic document device, determine whether the received handwritten signature for document confirmation matches the registered handwritten signature for document confirmation, complete the input of the handwritten signature in a signature field in the electronic document to be signed (S200-S210), generate an electronic signature value (DS1-DS3) by using the private key of the signer (U SK), and generate the encryption data (E1-E4) by encrypting the generated electronic signature value.