The invention discloses a direct torque control method and system based on a super-twisting sliding mode and an EKF observer, and the method and the system are used for controlling a permanent magnetsynchronous motor. The method comprises the following steps of measuring the currents ia, ib and ic and voltages ua, ub and uc of the output terminal of a three-phase inverter; converting a three-phase current and a three-phase voltage into currents ialpha and ibeta and voltages ualpha and ubeta in a static coordinate system, and then inputting into an EKF observer module, and estimating a statorflux linkage Psis, a motor rotating speed n, an electromagnetic torque Te, and a rotor position Thetae; calculating difference values between the stator flux linkage Psis and the electromagnetic torque Te and a stator flux linkage set value and an electromagnetic torque set value and inputting the difference values into the super-twisting mode, and controlling and acquiring the voltages in the static coordinate system; inputting the voltages in a SVPWM module, synthesizing an optimal voltage vector and controlling the switch state of an inverter so as to control the operation of the motor. Inthe invention, the control performance of the permanent magnet synchronous motor is increased, a torque ripple is reduced, and simultaneously the switch motion times of the inverter are decreased.