According to the demand of mechanized weeding in greenhouse, an intra-row weeding control system with disc-hoe was designed for electric drive weeding machine. The system, with the MC9S12DG128 binuclear MCU at its core, was composed of three Hall sensors and one rotary encoder, signals of which were real-time input into the MCU. The MCU received real-time visual signal of upper computer (PC) through RS232 serial port, and had a real-time communication with lower computer (motor drivers) via CAN bus. With the real-time control of rotation rate and rotation angle of disc-hoe, the control system realized intra-row weeding and seedling avoidance. The experimental machine included three disc-hoe units, and one land wheel on either side. Then the machine was connected to a tractor by a previa three-point suspension. The test results in greenhouse showed that the wounded seedling rate was within 10%, when the forward speed was about 1.2km/h.