The invention provides a method for securely accessing to protected resource and a system thereof, which belongs to information security field. A first terminal sends a request for accessing to the protected resource to a second terminal, and sends a user name and first data to the second terminal; the second terminal generates second data, and searches for a secret on a third terminal; the second terminal processes the first data, the second data, and the secret, so as to obtain a first characteristic value; the third terminal processes the first data, the second data, and the secret so as to obtain a second characteristic value, and upon receiving a confirmation message, processes the first data, the second data, and a secret pre-stored at/on the third terminal so as to obtain a third characteristic value; the first terminal sends the third characteristic value to the second terminal; the second terminal processes the first data, the second data, and the secret to generate a fourth characteristic value, and determines whether the fourth characteristic value is identical to the third characteristic value by comparison, if they are identical, accessing is permitted; otherwise, accessing is refused.