The invention relates to a stepping motor driving spindle servo control system and method for electric spark small hole machining. The system comprises a sampling circuit used for collecting a discharge gap voltage signal, a PID adjusting circuit, a voltage given circuit, an absolute value circuit, a phase discrimination circuit, a voltage comparison circuit, a subdivision code conversion circuitand a stepping motor driver, wherein the input end of the stepping motor driver is connected with the output end of the subdivision code conversion circuit. A mode of adjusting the subdivision numberof the stepping motor is adopted, so that the main shaft can be quickly fed or retreated in a manual operation mode, the driving subdivision number of the stepping motor can be automatically changed in a servo control mode, small-step equivalent feeding and large-step equivalent retreating are realized, and different requirements of the electric spark small-hole processing machine on operation ofthe main shaft in different working states are met.