The invention discloses a fractional frequency control method and system of a variable-speed wind power turbine. The method comprises the steps that a voltage signal and an electric current signal ofa power generator of the variable-speed wind power turbine are collected, and the electromagnetic torque output by the power generator is worked out; rotation speed information of the variable-speed wind power turbine is collected; according to the electromagnetic torque and the rotation speed information, based on inertia data of the variable-speed wind power turbine, the pneumatic torque estimator is worked out; the difference value between the pneumatic torque estimator and the theoretical optimal controlling torque is calculated, the torque controlling torque is built through a low pass filter according to the difference value, and finally, the torque controlling set value is obtained. The system comprises a voltage sensor, an electric current sensor, a rotation speed sensor, an electromagnetic torque calculating system, a pneumatic torque estimator calculating system, the low pass filter, a torque additional value building system and a torque controlling set value calculating system. According to the fractional frequency control method and system, the power grid friendly target that the smooth output power fluctuates on the power grid sensitive power section is considered, andmeanwhile, electric energy production is improved.