A joint guarantee system for vehicle assembly is applied to a vehicle assembly line that assembles an assembling object to a vehicle carried through on a conveyer line as an assembling element, and includes a vehicle detector that detects the vehicle entering the conveyer line, tool detectors disposed along the conveyer line that detect a position of an assembling tool on the conveyer line, an inertial sensor module installed in the assembling tool that detects an angle and a displacement of the assembling tool for an assembling point of the vehicle and the assembling object, a tool controller that applies control signals corresponding to a predetermined assembling point of the vehicle and the assembling object, a kind of assembling element, and assembling torque of the assembling tool, to the assembling tool, and a main controller that processes and stores the above information.