The invention provides an electric vehicle controller recognition control system and method and an electric vehicle. The system comprises a fingerprint recognition module and a controller, wherein the fingerprint recognition module comprises a fingerprint sensor, a fingerprint recognition chip and a first microprocessor, and the fingerprint sensor and the fingerprint recognition chip are sequentially connected with the first microprocessor; and the controller comprises a second microprocessor and a power tube unit, the second microprocessor is connected with the first microprocessor, a dynamic encryption algorithm the same as that of the first microprocessor is integrated in the second microprocessor, and the second microprocessor is connected with the power tube unit. The same dynamic encryption algorithms are integrated in the first microprocessor and the second microprocessor, it is guaranteed that each time a user starts the electric vehicle through a fingerprint, the impulse sequences sent out through the first microprocessor are different and can be accurately recognized by the second microprocessor, then the power tube unit is further controlled to be started, and the defect that conventional high and low level signals and fixed impulse sequences can be easily cracked is effectively overcome.