The invention discloses a variable-frequency power supply output negative-sequence voltage control method and a system thereof. The method is characterized in that the output end of an original variable-frequency power supply output voltage control loop is connected with a negative-sequence voltage control loop. The negative-sequence voltage control loop performs positive-and-negative sequence decomposition on a sampled variable-frequency power supply output voltage signal and obtains an AC-axis component and a DC-axis component of the negative-sequence voltage. Then the AC-axis component and the DC-axis component of the actual negative-sequence voltage are respectively subtracted from the given values of the AC-axis component and the DC-axis component of the negative-sequence voltage. The differences are transmitted to a deviation controller. Furthermore after Park inverse transformation, an outputting value of the negative-sequence voltage control loop is obtained. Finally the outputting value of the negative-sequence voltage control loop is superposed to the outputting value of the original variable-frequency power supply output voltage control loop, and furthermore controlling of the variable-frequency power supply outputting voltage is realized through pulse width modulation. According to the method and the system, the negative-sequence component of the variable-frequency power supply outputting voltage is used as a control object; the negative-sequence voltage control loop is increased for realizing controlling to the negative-sequence voltage; stability of the original control loop is not affected; and furthermore simple operation and easy realization are obtained.