In order to improve the assembly efficiency of large composite skin components, a kinematics inverse solution algorithm of 6-DOF flexible assembly mechanism based on three-point locating principle was put forward. Firstly, a kinematics model of the flexible assembly mechanism is established. And then three non-collinear measuring points coordinates on assembly parts were obtained by locating and tracking. In addition, the displacement of each driving joint was calculated by this algorithm. The simulation analysis of the virtual prototype model of flexible assembly mechanism is constructed by ADAMS software. It is found that the simulation results are in great agreement with the theoretical results, and the correctness of the algorithm is verified. Finally, the driving trajectory of the flexible locator is obtained through simulation. The results show that the algorithm was capable of keeping the assembly components move smoothly and precisely, which provided the technological foundation of accurate control for posture alignment mechanism.