The invention discloses an electric automobile theft prevention authentication method with communication data protection. In the method, the same fixing code and theft prevention secret key are storedin a motor controller and a theft prevention unit of an electric automobile, communication connection is established between the motor controller and the theft prevention unit, after a starting signal of the electric automobile is detected, the motor controller initiates a theft prevention authentication program, mutual verifying is performed between the motor controller and the theft preventionunit through multiple times of data communication transmission calculated through encryption and through combination with the fixing code and the theft prevention secret key, a communication data protection mechanism is added in the process of communication and includes data protection packaging and data protection unpacking, it is avoided that in the process of communication, data errors affect the process of theft prevention authentication, and the safety of theft prevention of the electric automobile and the reliability of the authentication process are effectively improved.