A control method and control system for an agitating mechanism are provided. The control method includes receiving a load current detected by a current detecting apparatus when the agitating mechanism is rotating along a specific direction; determining whether the rotation of the agitating mechanism meets a preset trigger condition based on the load current; and controlling the agitating mechanism to rotate in a direction opposite from the specific direction when the trigger condition is met. The present invention can reduce the possibility of the electrical components of the agitating mechanism being burnt out and prolong the lifespan of the agitating mechanism. The present invention can improve agitation results of the agitating mechanism. At low speed, the agitating mechanism can perform the agitation gently without damaging the texture of the solid food. At high speed, the agitating mechanism can more homogeneously and finely agitate the mushy food with enhanced agitating efficiency.