The invention discloses a foundation pit micro-deformation control system and method. The foundation pit micro- deformation control system comprises a hydraulic cylinder, a screw, a lock nut, a dust cover, an ejection block, a nut drive mechanism and a deflection prevention device, wherein the hydraulic cylinder comprises a cylinder block, a piston, a piston rod and a guide sleeve; the lock nut is screwed on one end of the screw; the piston rod can drive the screw to do linear telescopic movements; the nut driving mechanism is arranged on the screw; the nut drive mechanism rotates around the screw by driving the lock nut to enable the lock nut to cling on the dust cover to exert the effect of mechanical self-locking; the deflection prevention device is arranged between the cylinder bottom of the cylinder block and the piston rod, to prevent that the piston rod rotates so the lock nut cannot achieve the desired effect of synchronous rotation movement under the action of the nut drive mechanism. By applying the foundation pit micro-deformation control system and method, a gap between the dust cover and the lock nut can be removed, a real-time mechanical self-locking effect is exerted, waste of a large number of manpower and material resources is avoided, and the potential safety hazard is avoided.