The invention discloses a motor drive method and system of a pumping unit under an unconventional working system, and belongs to the field of oil production engineering. According to the method, a power frequency drive mode is adopted for whole-cycle operation of a crank, and a variable frequency drive mode is adopted by non-whole-cycle pumping operation of the crank and non-whole-cycle non-pumping operation of the crank. The system is provided with a power frequency circuit and a variable frequency circuit with common input and output, wherein input ends of the power frequency circuit and the variable frequency circuit are connected to a power frequency power supply circuit and output ends are connected to a drive motor of the pumping unit; a frequency converter is arranged on the variable frequency circuit; and an operational control unit is also arranged outside the power frequency circuit and the variable frequency circuit. By the motor drive method and system, motor drive means of the pumping unit under the unconventional working system are provided; the actual working time of variable frequency drive can be shortened and the working intensity of the frequency converter can be reduced under the condition that the actual production speed requirement is not equal to a power frequency speed; the heat dissipation condition of the frequency converter is effectively improved; and the equipment lifetime of the frequency converter is prolonged.