The instant disclosure provide a gastrointestinal tract diagnosis system, at least comprising: an endoscope having a magnetic plate therein, the magnetic plate having a first magnetic pole and a second magnetic pole respectively distributed at a lower half portion and an upper half portion defined along a thickness direction; and a magnetic control device including: a magnetic stick including a first electric magnetic pole at a terminal portion of the magnetic stick and a second magnetic pole located at a base portion of the magnetic stick; a magnetic force output module for being used to output a predetermined current to the magnetic stick so as to allow the magnetic stick to generate a predetermined current for interacting with the first magnetic pole and the second magnetic pole; and a magnetic force feedback module, wherein the predetermined magnetic force is for drawing the magnetic plate to control the movement of the endoscope, the magnetic plate causes a feedback magnetic force to a sensor of the magnetic stick, converting the predetermined current into an offset current, and the magnetic force feedback module calibrates the offset current, resuming the offset current back to the predetermined current, so as to stabilize the predetermined magnetic force. A control method for the gastrointestinal tract diagnosis system is also disclosed.