The invention discloses a control method used for a cutterhead driving system of a shield tunneling machine and based on driving shaft torque estimation. The control method comprises the steps that firstly, a cutterhead driving system mathematic model containing backlash nonlinearity is established; then the cutterhead driving system mathematic model is linearized and simplified to obtain a statespace model; and then the rotating angular acceleration is introduced into a state variable, so that a cutterhead driving system augmented model is established; the estimation algorithm of the drivingshaft torque is designed according to a kinetic equation of the cutterhead driving system; finally, taking the cutterhead rotating speed tracking error and the driving shaft torque uneven distribution degree as the performance index, a model predictive controller is designed, and control over the cutterhead driving system is achieved; and a state observer is designed so as to realize estimation of the rotating angular acceleration. According to the control method, through driving shaft torque estimation and combined with the model predictive controller, meanwhile, cutterhead rotating speed control and driving shaft torque balance control are achieved, and the system has better anti-interference ability and robustness.