The invention discloses a special motor control system for an intelligent channel system and a control method. The motor control system comprises a main control circuit, a motor driving circuit, peripheral equipment and a detection module, wherein the main control circuit comprises a DSP (Digital Signal Processor) and an FPGA (Field Programmable Gate Array) processor; the motor driving circuit comprises a driving module and a semi-axle circuit; the peripheral equipment is connected with the FPGA processor by a third I/O isolation module, and comprises an infrared sensing module, an access module and a clutch module; and the detection module comprises a temperature sensor, a current detection module and a position detection module. According to the invention, by monitoring for the position, speed and current of a motor, adoption of a closed-loop feedback technology with a high-resolution encoder as well as optimization of speed setting and a acceleration curve, the starting speed is high, the stoppage is smooth, and the mechanical noise is reduced, so that the special motor control system can be applicable to occasions with very-frequent passage.