The invention provides a pressing plate controlling system and method of a pocket-hole sewing machine. The pressing plate controlling system of the pocket-hole sewing machine comprises a signal collection unit, a pedal monitoring unit and a middle pressing plate controlling unit. When the signal collection unit collects a signal that hands of people enter between a middle pressing plate mechanism and a presser foot mechanism, the middle pressing plate controlling unit outputs a signal for stopping work of the middle pressing plate mechanism. When the signal collection unit collects a signal that no hands of the people enter between the middle pressing plate mechanism and the presser foot mechanism and the pedal monitoring unit monitors that a pedal mechanism is pedaled, the middle pressing plate controlling unit outputs a signal for starting the work of the middle pressing plate mechanism. Due to the existence of the signal collection unit and the pedal monitoring unit, when inserting the position between the middle pressing plate mechanism and the presser foot mechanism, the hands of the people is sensed by the signal collection unit so that no industrial accident can be caused even if the pedal mechanism is pedaled mistakenly. The invention further relates to the controlling method.