In this paper, an adaptive artificial potential function (AAPF) method is developed for spacecraft formation reconfiguration with multi-obstacle avoidance under navigation and control uncertainties. Furthermore, an improved Linear Quadratic Regular (ILQR) is proposed to track the reference trajectory and a Lyapunov-based method is employed to demonstrate the stability of the overall closed-loop system. Compared with the traditional APF method and the equal-collision-probability surface (ECPS) method, the AAPF method not only retains the advantages of APF method and ECPS method, such as low computational complexity, simple analytical control law and easy analytical validation progress, but also proposes a new APF to solve multi-obstacle avoidance problem considering the influence of the uncertainties. Moreover, the ILQR controller obtains high control accuracy to enhance the safe performance of the spacecraft formation reconfiguration. Finally, the effectiveness of the proposed AAPF method and the ILQR controller are verified by numerical simulations.