The invention discloses a flexible start intelligent transmission system for a coal mine scraper conveyor. The system comprises a soft start permanent magnet device, a chain tightener and a reduction gearbox; an input shaft of a motor of the scraper conveyor is in spline connection with an input shaft of the soft start permanent magnet device; a transmission shaft of the soft start permanent magnet device is in spline connection with an input shaft connected with the reduction gearbox; the chain tightener is in spline connection with the transmission shaft of the soft start permanent magnet device; when the scraper conveyor is started, the motor drives a conductor disc to perform a magnetic force line cutting motion in a strong magnetic field generated by a permanent magnet disc; eddy current is generated in the conductor disc; an induction magnetic field is generated around the conductor disc by the eddy current to stop relative motions between the conductor disc and the permanent magnet disc so as to realize torque transfer between the motor and a speed reducer; during starting, soft start is realized through prolonging the rotating speed balance time between the conductor disc and the permanent magnet disc; and when the load of the scraper conveyor reaches a protection torque value set by the permanent magnet device, the rotating speed of the permanent magnet disc is lowered to realize overload protection, and the damage to equipment by overload is prevented.