A flexible surgical tool system comprising a multi-degree-of-freedom mechanical arm, the flexible surgical tool, the remote control device and a controlling computer is provided. A method for controlling the same with motion constraints is also provided. The method can comprise: obtaining a target posture of the surgical actuator, a current posture of the surgical actuator and bending angle values of the sections of the flexible surgical tool. A desired velocity of the surgical actuator and a motion limitation condition can be obtained. Joint velocity of the multi-degree-of-freedom mechanical arm and bending velocity of the sections of the flexible surgical tool can be obtained. A target joint position value of the multi-degree-of-freedom mechanical arm, a target bending angular value of the sections of the flexible surgical tool, and transmitting them to a corresponding controller to drive each section can be obtained. The above operations can be repeated.