A vehicle control apparatus and a control method thereof are provided. A vehicle control apparatus includes a processor including a host core and a hardware security module (HSM) core. The processor generates a first private key and a first public key, receives a second public key from a diagnostic device, generates a shared key based on the first private key and the second public key, receives a security data transmission request from the diagnostic device, and encodes data based on the shared key and transmits the encoded data to the diagnostic device.