A method of performing cross-authentication in a vehicle controller interworking with an external device includes: generating a random number S and transmitting the random number S to the external device according to an authentication request message received from the external device; generating a variable i using a first function having the random number S as a parameter; generating a first session key Ks using a second function having the variable i and a pre-stored secret key K as parameters; receiving a first response key from the external device; generating a second response key using a third function having the random number S, the variable i and the first session key Ks as parameters; and authenticating the external device based on whether the first response key is equal to the second response key.