The invention discloses a self-adaptation flexible assembling and calibrating system based on a mechanism. The self-adaptation flexible assembling and calibrating system comprises a rack, a Z-axis lifting mechanism, a supporting plate, a space microgravity five-freedom-degree self-adaption flexible adjusting mechanism and a locking mechanism. The supporting plate is adjustably arranged on the Z-axis lifting mechanism. The space microgravity five-freedom-degree self-adaption flexible adjusting mechanism is fixed to the supporting plate. The Z-axis lifting mechanism drives the supporting plate to move vertically so as to achieve the freedom degree of the movement along the Z-axis straight line. The locking mechanism is fixed to the space microgravity five-freedom-degree self-adaption flexible adjusting mechanism so that the self-adaptation flexible assembling and correcting system based on the mechanism can achieve accurate butt joint of one butt joint part and one part to be subjected to butt joint. The self-adaptation flexible assembling and calibrating system based on the mechanism can meet the requirement that the structure is simple, the bearing capability is large, and the self-adaptation flexible assembling and calibrating system can adapt to various outline specifications of an assembled and calibrated object.